Unfortunately, there is currently a known bug (which should hopefully be fixed in the next version of Juicebox) whereby the value of the expandInNewPage configuration option can change the scale of the embedding page. This may be the cause of your problem.
If your gallery currently sets expandInNewPage="TRUE", then try setting expandInNewPage="FALSE" (in JuiceboxBuilder-Pro's 'Customize -> General' section). Conversely, if your gallery currently sets expandInNewPage="FALSE", then try setting expandInNewPage="TRUE".
(Alternatively, try setting expandInNewPage="AUTO" if "TRUE" or "FALSE" do not work.)
As I noted, we hope to have this bug fixed in the next version of Juicebox but, in the meantime, changing the value of expandInNewPage should help.