Having two Tinkertools in your inventory, trying to fix one of them to 100% will always result in "You repaired the Tinkertool to 99 percent." and the Tinkertool's stats to be 199/200. Trying to wear down the Tinkertool and fixing again doesn't help either.
Have a look at the following screen recording that demonstrates the issue:
http://dl.dropbox.com/u/3813676/tinkertool_stuck_at_99_percent.mov (8 MB) - 1/2 size
http://dl.dropbox.com/u/3813676/tinkertool_stuck_at_99_percent_large.mov (23 MB) - full size
This was recorded in Google Chrome 13.0.782.215 on Mac OS X 10.6.8 (Snow Leopard) but I tested it on other browsers (Firefox) and OS X 10.7 too with the same result.
The recording is from the last test, but it is still the same in the current version.