I have one doing the same thing! Hi-Res or interlace screens it flickers like crazy when there is disk or HD access! Lo Res its fine! Gotta try this hack.
My brother's old A1200 had this problem -- it was a bug in that particular board revision I think, mine didn't have the issue. The fix? Eliminate any colours in the screen's palette set to 255,255,255 (full white)!! Bizarre, I know, but it did the trick for his machine -- he even wrote a little daemon to monitor the palette of the top screen and adjust to 254,254,254 any such offending colours!
