I have updated to B6 and the problem has come back. I did some more testing in case it is of some use.
1. I created a clean config and tried to reproduce the problem, I could not. I then went back to my original config and the problem STILL existed--unlike my previous B4 results.
2. Within my original config I created a new Lua file and the problem did NOT reproduce.
3. Going back to the original file (original config) I STILL have the problem.
Bottom line it seems that it might be related to editing an existing buffer/file. I have not been able to find a workaround yet.
I have also found a slight variation to my problem. If I comment both lines below, then just toggle-comment on an highlighted (or not) line I get indenting problems. I also tested this problem on an existing buffer within a C file and it is a problem. Not 100% reproducible in my C file, but around 75%.
Lua example:
Start with:
-- if something == true then
-- do_it = true --<<<<< cursor on this line
After just running toggle-comment without highlighting a line I get:
(seems to also be a problem if highlighted)
-- if something == true then
do_it = true
NOTE: Sample problem in C, but not as reproducible
NOTE: Not just an "if" statement specific problem.