Yes, it's because of the recent commits.
I already spoke to ghazan about it and it _should_ be fixed in
https://github.com/miranda-ng/miranda-ng/commit/32ac77ea600fa6ae33fea77d2be8fdaec865da7b , i.e. if you update today it should be okay.
Duplicate contacts will however remain duplicated.
if you don't have a backup, then:
1) shut down miranda
2) make a copy of your .tox and miranda profile
3) start miranda
4) delete the duplicate contacts - they won't have any message history and will have high numbers in dbeditor.
5) shut down miranda
6) put your tox file back (yep)
7) start miranda again... should be all good now with working tox and with dupe contacts gone. I recommend running a dbchecked afterwards just in case.
This is what I had to do with friend's miranda after his contacts got quadrupled...