The best way to overcome these little glitches, is to pinpoint the problem areas of the design, then write specific rules squash the bug. You then extract these rules out into a separate stylesheet and call them up with conditional comments. This way you can target the desired version of IE.
Yeah its a bit annoying, but take heart... IE 6 onlly has like 35% of the market now and is rapidly losing ground to Firefox.. combine this with the fact that IE 7 is default browser of Vista and there will be even less motive to trouble yourself with IE 6 in the near future.
For now, it is what it is.