I ran into the same problem yesterday.
My temporary solution was to comment out the MIN_LIMIT and MAX_LIMIT lines in the .ini file. This doesn't give an error message. Clearly, there is some default limit, but I don't know what that is. At least I was able to finish my run (which needed about 60 turns) without running into the 9999 limit.
I tried the WRAPPED_ROTARY option (which sounds like just the right thing). However, I had nothing but problems with that approach. The first thing I discovered was that G90.2 and G91.2 don't work like the wiki documentation says. Use of G90.2 or G91.2 gives an error message. The next thing I discovered was that you can't make a full turn or more. You can only turn something strictly less than 360 degrees. Then I discovered that going to a negative rotation gives you something other than what you would expect. For example C-90.0 goes 3/4 of a turn to the equivalent position of 270 degrees (but turns in the opposite direction). This is really counter-intuitive -- I'm thinking that C-90.0 should give only 1/4 of a turn. The real killer for me was that wrapped rotary options in EMC2 and MACH3 behave totally different. So developing software that generates g-code that will run the same on both EMC2 and MACH3 is impossible if you use wrapped rotary axes.
If there are any other solutions, I would be most happy to hear.