Have you tried leaving the wallet closed on one of your windows machines for a couple of weeks so it's forced to do a resync?
Yes and it usually works fine.
EXCEPTION: N5boost10filesystem16filesystem_errorE
boost::filesystem::remove: The process cannot access the file because it is being used by another process: "C:\coins\cryptonite\blocks\index\000081.sst"
C:\coins\cryptonite\win64_cryptonite-qt_14091021.exe in Runaway exception
The good news is you've provided a descriptive error message to help pinpoint the issue. The bad news is this seems to be a problem which has exist for several years in other altcoins such as litecoin and still hasn't been fixed:
https://litecointalk.org/index.php?topic=10746.0EXCEPTION: N5boost10filesystem16filesystem_errorE
boost::filesystem:remove: The process cannot access the file because it is being used by another process: "C:
\Users\Owner\AppData\Roaming\Litecoin\database\log.0000000001"
C:\Program Files (x86)\Litecoin\litecoinqt.exe in Runaway exception.
My naive guess would be that you might have cryptonited already running in the background or something.