After hitting ctrl+D with the find window open, regex matching won't work until either find is closed and reopened, or regex disabled and reenabled.
Hit ctrl+F, search for a regex with regex mode enabled. E.g. search for "\blime" in this:
Now hit ctrl+D. The regex is ignored ("\b" is removed from the search box, and both instances of "lime" are selected). This is somewhat annoying, but it's not the bug.
Now change the search box to a regex again ("\blime"). It comes up with zero results. Even if you completely remove the text in the search box and search for other things, it'll interpret everything as pure text. Regex matching won't work until the find window is closed and reopened, or regex disabled and reenabled.
Sublime 3 3033, Linux