There is a compression to consider when making BD menus. Although I've worked on several for many years, I don't author them. I only design, animate, then send elements out per spec to clients. If your transitions are extremely different from your MM or Loop, make sure you check your Color Management preferences & your delivery spec, they might deliver an animation that appears different from your Photoshop design comp.
Make sure your MM and Loop are rendered with the same codec that your transition is rendered with?
Double check to see if there's a strange alpha left in your transition?
Checking the emulation will probably give you the best QC for color.
Without screenshots or that exact file it is a little bit of a guessing game to help you. But maby it is because of a compression of that transition. I'm guessing that your menu is a static file (psd,jpg,png etc.) and transition is a video file (mp4, mpeg etc.) if that is the case the difference in colour will be caused by video compression. The reason why you are seeing that difference in some players and can't see in others is because different playres uses different encoders (codecs) that interpret colours differently.
Is there anything in the project files that maybe causing the colour issue?