Thanks Peter. The *.* wildcard seems to have done the trick.
I added both of the exclusions you suggested, and re-installed GDFS. This configuration works fine.
I then went back and removed the exclusion that specifies my username rather than using a variable. It still worked fine.
For reference, here's the exclusion set that I'm currently using:
/Volumes/GoogleDrive/*
/Volumes/GoogleDrive/*.*
/Users/%user%/Library/Application Support/Google/DriveFS/*
/Users/%user%/Library/Application Support/Google/DriveFS/*.*
/Users/%USER%/Library/Application Support/Google/DriveFS/*
/Users/%USER%/Library/Application Support/Google/DriveFS/*.*
So far, it's working fine with GDFS. I'm sure some of these rules are redundant... with more testing I'll probably be able to remove two or more.