Did someone manage to create a colour combination (View > Appearance > Colors) that allows you to recognise the boundaries of your source terms from your glossary?
(I wouldn't mind to not see the green colour for the fragments at all, personally I find them distracting.)
My Source segment:
Two entries from my glossary:
As you can see: there's no way that I can see that both entries are being used here for auto-assembling. Overlapping/colour matching clash?
Here's another example of what I mean:
One could suspect that 'die linke Mastaste loslassen' is actually a glossary entry. However, it consists of two other entries:
How about changing the term match font color to a color other than black?
It gives you double information at the same time.
The first thing I usually do when installing CafeTran is activate:
View > Colours > Hide memory match colors in the source segment
This leaves only the glossary matches highlighted.