Two things spring to mind that could cause the problems you're having.
One is a dry solder joint. Funny enough I did exactly the same with my MK3 when I changed the batteries. Had me going for a minute or two as to why is wasn't working reliably, but a quick prod with a soldering iron to melt the solder holding the batteries in and letting it freeze again sorted out the problem. The problem has never returned.
Secondly, much more worrying, is that they really have 'made it a new gun' by flashing new software on it, which has an almightly software bug. If that's the case, it really is broken until you get some older more reliable software back on it.
In either case, Daystate should be sorting it out free of charge. You've already paid far more than it could ever be worth to swap out those batteries. From memory (it was a couple of years since I did mine) there are a couple of PCB mount cells in there, no more than £35 quids worth of parts posted from any internet place that stocks them. I reckon the job would have taken them less than 10 minutes.
Longer term, I have to confess that our household doesn't use the daystate for comp shooting at all anymore. I honestly feel that from my experience with mine they just don't measure up in FT. I base that soley on the fact that it seems to consistently drop pellets by exactly two mill dots at least 1 in 10 shots. Furthermore, I'd say that Styer doesn't measure up either, but I'm biased due to my much worse experience with an LG110 that I owned briefly a few years ago that simply would spray pellets all over the place on hot days.
I don't mean to stir up anything by saying these things. I can't deny that some brilliant shooters out there (far better than I) have had a lot of success with both makes of kit that I've had bad experiences with. I'm only saying it in the hope that you're not completely sold on the Steyr until you've looked at Anshutz and perhaps an EV2 (the two guns that have been serving me and the misses well since we bought them).