Ok -
A) don't worry, it's NOT a big deal.
B) The problem is most likely easily fixable if what I think happened, happened.
Here's what's most likely happened:
When you formatted the thumb drive w/ disk utilities it was set to use a GUID partition table scheme. On a Mac this isn't a big deal - on a PC, well it's a different story - when formatted with this scheme you end up with 2 partitions - a tiny one (that comes first in the partition table, but is invisible on OSX) and your main one. Windows doesn't like thumb drives with multiple partitions, and will see the first small partition, claiming the drive isn't formatted, then once formatted, you end up with a 200meg drive - if you use the manage tool in windows and go to the drives section, you'll see the drive there with the multiple partitions.
put your thumb drive back in your mac, go to disk utilities, go to partition, select 1 Partition, make sure it's set for FAT32, and on the bottom, click options, make sure to change the partition table to master boot record. apply the changes.
That *should* fix the problem. I had a similar problem when I reformatted a thumb drive and didn't think to check the partition table scheme, changed it and repartitioned and it was good again.