Well I can't say how or why it does this as I used dltcep to create the 'mirror' images (the ones that end in E) and never bothered to re-open them in BAMWRKSHP I or BAMWRKSHP II but if your interested in changing any of the BAMs by size or color I have a simple solution.
Load the original animation lets use MXXXWK (walking animation) for an example.(these should load just fine in your BAM editor of choice)
1) load MxxxWK into BAMWorkshopI, or BAMWorkshop II, make changes with color,contrast,size,etc...then RE-SAVE the bam.
2) Load the BAM you just re-saved into dltcep and choose the "create mirror image" ...1-2 seconds later you will have the MxxxWK(e) version of your customized creature. then re-save using dltcep (it will automatically append the E at the end of the animation.
3) try your new customised BAM in your game
(NOTE: to those that might not know already, but the (E) versions of the animations are nothing more then the original animation but 'mirrored' to create the east facing animations (Northeast,East,and Southeast) . So if you load the BAM mentioned above (the MxxxWK) in BAMW just to preview it, you shouldn't worry too much about seeing what the MxxxWKE looks like because...well...its exactly the same just mirrored. I used dltcep because it skimmed about 1 hour off the time to create these eastfacing animations.)
I hope that helps, perhaps Avenger (dltcep's creator can offer more light on this subject of errors)