I'm not surprised by the 'fancy window layering' being something of a lash-up. A few days ago I tried to load Word 2007 on a machine that was labouring under an update and had slowed to a crawl, only to discover that under the 'Office button' etc lies a rather standard Window, with the fancy stuff simply drawn on top. From what you say, Aero is also 'drawn on top'.
Can't you arrange your toolbar design so that the bubble help appears over something uncomplicated (e.g. by using an appropriately deep %bx)?
You mentioned the 'arrow section' on 'bubble-style'. This suggests that you are using %bh. I found that I didn't like the thick border with this, and I prefer %th or %th. Do they give you a better effect? (%`bh puts the bubble-and-spike much further away from the toolbar icon, %th is closer, so that your mouse pointer effectively provides the 'spike'). When using %th help strings, I find that I prefer them to start and end with a blank. I also find that %?ib@ gives me trouble that %ib followed by options and then help strings doesn't, whereas %?tb@ works fine (FTN95 4.90).
Eddie