Thanks. Today I’ve compared my JT-4000 to another unit which a friend of mine owns, and came to conclusion that this bug affects all of the units running new firmware. Besides envelope issues, it has turned out that actual BPM present on ARP page is not even real.
It’s a pity that Behringer even has no dedicated user forum or just a form for users’ feedback, so I’ll keep searching for submitting my own.
P.S.: A user who built an excellent software editor for Reaktor ensemble has mentioned on Native Instruments library that they’ve improved envelopes in new firmware build, that gives us a hope they could fix clock issues in further firmware updates.