@Ann
Thanks for sharing your recent experience.
Backing up important files is definitely recommended (and can often turn out to be essential) but automated systems such as iCloud can be backing up stuff without people being aware of what is going on (and this can cause slow-downs or, in the case of JuiceboxBuilder, problems).
Similar problems can happen with OneDrive on Windows PCs.
I help a lot of friends with their PCs and the majority have no idea what OneDrive is, let alone what it is doing. OneDrive quite often backs up files that my friends have no interest in having duplicates of. My friends often contact me when they get a message saying that their OneDrive storage is full and wonder what is going on! This might not be representative of Juicebox-Pro users but it's a problem I encounter frequently.
Maybe it's for the best that locations like default 'Documents' folders are being backed up automatically (backing up a lot of unwanted files at the same time). At least the important files are being backup up.
Having said that, it's important to know what locations are being backed up so that problems (such as the JuiceboxBuilder one) can be worked around.
Ideally, JuiceboxBuilder should maybe choose a different location for its temporary work folder (knowing that iCloud and OneDrive backup the system's 'Documents' folder by default) but that would require a recompiling of the application and unfortunately, I don't see an update forthcoming.
In the meantime, the best course of action (as you have discovered), is to ensure that iCloud (or OneDrive or any other online backup service) is not backing up any locations used by JuiceboxBuilder (i.e. the 'Documents' folder and the folders you choose to save galleries to).
In any case, I'm glad you're able to use JuiceboxBuilder without all the problems and frustration that iCloud was causing!