thanks for the quick portabilisation of the new SeaMonkey release. You have been even faster than the German SeaMonkey support team that doesn't say anything about release 2.39 on it's website.
But: After the automatic PortableApps platform update, SeaMonkey's "about:" window still tells 2.38. None of the extensions (particularly Lightning) complains about a new version. Looks like the PortableApps "update" version still is 2.38 by mistake.
Manually installing the PAF package downloaded from you website worked fine, I finally got SeaMonkey Portable 2.39.
The platform pulls from the exact same place as the website. Same files. Same MD5 hashes. All are version 2.39. All contain a seamonkey.exe version 42.0 (since it's based on Firefox's versioning internally).
I just updated 2.38 to 2.39 via the updater in German and it updated as expected. And nothing has changed about SeaMonkey's files or entry in the database since the day it was released.
Only thing I can think of is if you have two copies or an oddball directory or something.
Sometimes, the impossible can become possible, if you're awesome!