Currently about:addons tells me the userscript is version 2.21.1 while in reality (when editing the script and looking at the source) it's 2.21.4
Environment: Nightly 11.0a1 (2011-11-27), Greasemonkey 0.9.13
I restarted for today's Nightly update, and I noticed that now the version is displayed correctly. I also updated a different userscript (by manually installing the newer version from US.o) and the same problem manifests.
So confirmed, with Greasemonkey 0.9.13. And 2011-12-03 nightly.
Keep the AOM up to date when re-installing a script.
I.E. installing to update to a new version.