There seems to be a problem with the rule "0/something/conditions". The specific example is:
/˧˥/V(ː)_(C)[pts]
[pts]//T_ (T being "tone")
When this is applied to "ukta" it results in "u˧˥ta", but when applied to "ut" results in "u" when it should produce "u˧˥". I managed to work around this problem using this:
/˧˥/V(ː)_[pts]
/˧˥/V(ː)_(C)[pts]
[pts]//T_
So the source of the trouble appears to be that (C). I tried replacing /˧˥/ with /z/ and [pts] with "t"; the rule didn't work as it should have, meaning that it's definitely the "(C)" that's causing the problem. Oddly enough though, the rules
/ː/V_(C)s
/˧˥/Vː_(C)s
work just fine. So perhaps it's the "(ː)"?