you've tried removing the theme styles using the "remove all styles" button in the inspector, correct? (under the appearance tab).
It seems that charting is a core feature of your solution, and you may want to hold off migrating until you can either come up with an alternative in 12, or fix the issue through trial and error.
Not really relative, but I've done a similar style bar graph in past-days using conditionally formatted text blocks. Not as good as charting, but I was able to control the block size down to a much smaller line height and width.
Yes, all styles removed. We have also considered going back to the FMP6 method of using strings of '"|" characters. Its looking very much like this is what we will have to do. Very sad. The addition of charts was such a big deal in 11. And although they've added a few new features in 12, this change to object characteristics has really ruined things for us. Just to illustrate the point further Ive attached a comparison of sizes between 11 and 12. The disaster here is that the object extends way up above the top of the actual chart, and in order for the object to render properly the top handles must be inside the summary part. So this does not work at all in 12. Its really quite crude compared to 11.
Well, I'm not discounting your problem here, but I've seen a lot of benefits in filemaker 12's direction and interface. It certainly was a "your mileage may vary" kind of update for a lot of developers and a lot of pre-made solutions. The entire front-end rendering of layouts in filemaker 12 is different, as in it's now rendering layouts using a web-like html/css-like engine. While we gained a lot (curved corners, gradient fills, multi-state styles, etc..) with this new frontend, there are cases, such as yours, that seem to deal with a lot of frustration in change. Given the file format change though, this is the direction filemaker is going for the foreseeable future.
Perhaps you need to start looking at alternatives to the native chart objects, and decide if the advantages you can realize from FM12 (IE ExecuteSQL chart data, long-term viability), are worth the time investment to upgrade. You can still do charting via a web viewer ( IE using google charts as a web service). It might also be worth it to invest in some consulting time from some industry experts that do consulting work (IE soliant, seedcode, etc..)
Fortunately from my talks with filemaker, it still seems like they will be allowing licensing of 11 to continue for a while, which should give you plenty of time to work out a viable solution in the fmp12 format while still selling your robust 11 solution for now.