FWIW, I noticed the same issue on two of my three machines with 060 accelerators:
2000 w/ Blizzard 2060 and Spectrum 28/24
- FBlit, Picasso96, PowerIcons
1200 w/ Blizzard 1260 (AGA only)
- FBlit, BlazeWCP
4000 w/ CyberStorm MKIII and Picasso IV (NOT affected)
- FBlit, P96, PowerIcons
I do not believe I am using anything other than the default configs for FBlit, and have followed the docs on startup placement and WBPrefs settings. All have 2MB Chip and >= 128MB Fast. I will have to check on the configurations for each program, as well as the versions. I hoped this might be helpful in finding a common thread.