The problem you are describing sounds like a known bug whereby main images may not display when selected in IE8 and IE9 when imageTransitionType="SLIDE" (which is the default value for imageTransitionType, used by Juicebox-Lite).
This bug has already been addressed and will be fixed in the next version of Juicebox.
If you were a Juicebox-Pro user, a workaround (until the bug is fixed) would be to set imageTransitionType to something other than SLIDE (e.g. FADE, CROSS_FADE, NONE).

The 'Active X' warning is not related to the problem (above) and should be displayed only when the gallery is run locally (from your hard drive) and not when the gallery is uploaded to and run from your web server.
You can disable this warning in Internet Explorer (so that you do not need to click 'Allow Blocked Content') by going to 'Tools -> Internet Options -> Advanced (Tab) -> Security' and selecting 'Allow active content to run in files on My Computer' and clicking 'OK'. (A browser restart will be required.)

As long as you are referring to the normal rather than fullscreen (expanded) gallery display, then you can set the gallery's width to be 90% in the embedding code and horizontally center the gallery's div in its parent container as follows:

<!--START JUICEBOX EMBED-->
<script src="jbcore/juicebox.js"></script>
<script>
new juicebox({
    containerId: 'juicebox-container',
    galleryWidth: '90%'
});
</script>
<div id="parent">
    <div id="juicebox-container" style="margin: 0 auto;"></div>
</div>
<!--END JUICEBOX EMBED-->

No matter what the height of the gallery is, Juicebox will respect the aspect ratio of the main images as long as imageScaleMode is set to SCALE_DOWN or SCALE.

I hope this helps.

The default metadataExportMode value has changed from 'All' to 'Copyright Only' but all you need to do to change it to 'All' is scroll down to the 'Metadata' field in the 'Output Settings' section, click on the 'Copyright Only' label (to reveal the drop-down menu) and select 'All'.

I'm glad you've been able to resolve your problem.
Thank you for posting back to let me know.

Incidentally, you would have a Transaction Id only if you purchased Juicebox-Pro via PayPal. (You would not have a Transaction Id if you paid with a credit card via Gumroad.)

The 'full.html' file should find the gallery's XML file as specified by your configUrl.

Please make sure that that your gallery uses the current version of Juicebox-Pro (v1.4.2) to ensure that any bugs which were present in previous versions but which have since been fixed are not contributing to your problem.
If necessary, instructions to download the current version and upgrade existing galleries can be found on the Upgrading Juicebox support page.

If this does not help (or is not relevant), then please post the URL to your gallery's web page so that I can take a look and help further.

The 'full.html' file contains no PHP code so there is no need to change the extension of the 'full.html' page. A web site can happily contain a mixture of both HTML and PHP files.
In any case, the 'full.html' file cannot be renamed as it is referenced from within the 'juicebox.js' file which is obfuscated and cannot be modified.
Under normal circumstances, there should be no need to modify (rename or move) any files within with 'jbcore' folder.

The 'full.html' file is used when a gallery is expanded on a page of its own. This will happen when expandInNewPage="TRUE" or when expandInNewPage="AUTO" and an iOS device is detected. Please see the Expand Gallery Behavior support section for further information.

That's great to hear! I hope you enjoy using Juicebox-Pro.
Setting expandInNewPage="TRUE" in JuiceboxBuilder-Pro's 'Customize -> General' section is certainly the easiest way to solve the problem until the next version of Juicebox is released with the bugfix.

That's great!
Thank you for posting back to let me know.

I notice that your gallery uses Juicebox-Pro v1.2.0.
Please upgrade to the current version (v1.4.2) and your problem should be solved.
There was a bug in v1.2.0 affecting 2-image galleries which was fixed in v1.3.0.

Instructions for downloading the current version and for upgrading existing galleries can be found on the Upgrading Juicebox support page.

Yes (although this should not be necessary).
What you are describing is actually a known bug whereby elements which have explicitly been assigned a CSS 'position' are not covered when the gallery is expanded either from the Splash Page or by clicking the Expand Button (they should be). This bug has already been addressed and will be fixed in the next version of Juicebox (although I do not know when it will be released).
In the meantime, the workaround (for Juicebox-Pro users), is to set expandInNewPage="TRUE" so that, when the gallery is expanded, it is displayed on a page of its own rather than on top of the embedding page.

Each user will have different requirements and, in resizing images, it may help to know the target audience.
For example, if your gallery is likely to be viewed on a mobile device, then you could probably get away with having much smaller images in your gallery than if the gallery is likely to be displayed on a large desktop monitor (the content of the images and web site may play a part in determining this).
The default values in JuiceboxBuidler-Pro usually result in a good compromise between size and quality for most users (or at least a good starting point for the values to be tweaked).

Personally, I convert my own RAW images to JPEG and then feed these JPEG images to JuiceboxBuilder.
The source JPEG images are approximately 10MB each and, using the default 'Large Images' settings of 2048 x 1536 at 80%, the resulting large images are approximately 400KB each. The resulting image look good enough for me (although I understand that everyone will have their own opinion as to what is 'good enough' for their own galleries).

I do not know exactly how JuiceboxBuilder-Pro internally resizes PNG images (using whatever resizing library or algorithm that Adobe AIR provides) but the only user controls are the dimensions and quality settings.
It looks like you would have much smaller (file size) images if you worked with JPEG images from start to finish.

As long as your source images are of a high enough quality, it is unlikely that the images used in your gallery would be visually unacceptable (especially if you kept the quality setting high enough).

Otherwise, you could always create your own set of large images in Photoshop and copy them across into your gallery's 'images/large/' folder. It might be an extra step in your workflow but if it results in a gallery that you are more happy with, then it might be worth doing.