(edit - sorry lokki, meant to post it to Technobear or the list in general)
I've the same problem (Linux mint 18 based on Ubuntu 16.04, Mate edition).
Sync (checkout) FAILED : factory (1.0.11,anon)
Current factory library does not match correct version, upgrading master -> 1.0.11
Changes stashed successfully: factory (1.0.11,anon)
upgrade (fetch) FAILED : factory (1.0.11,anon)
My Java info is
$ java -showversion
openjdk version "1.8.0_91"
OpenJDK Runtime Environment (build 1.8.0_91-8u91-b14-3ubuntu1~16.04.1-b14)
OpenJDK 64-Bit Server VM (build 25.91-b14, mixed mode)
Whenever I start Axoloti I'm told I have a user version mismatch and do I want to upgrade? Answering yes or no results in the same behaviour next time I start (I get the same error box and option to upgrade or not).
I saw that ~/axoloti-factory or contribs were empty so I copied old versions in but I still get a long list of Java errors (and numerous things to do with duplicates which is presumably related to this unmanaged lib copying):
Original name: wave/play fn
Duplicate UUID! ~/axoloti/objects/wave/play fn.axo
Path: ~/axoloti/axoloti-factory/objects/wave/play fn.axo
I hope that is of some use to someone!