I've just had a similar experience. Perfectly normal ecgs for donkeys years and this new machine's software now says error or somesuch so my AME can't issue a certificate and the reading has to go to CAA for the cardiologist to read. I posted it off last Tuesday and called CAA today, a week later, to confirm they had received it. A charming lady checked and said it would be read tomorrow and I should get a letter next week. She apologised for the delay, saying "..so many of you are showing anomalies".
To my mind, this is proof enough that the software isn't up to the job. Given the stress that such an occurrence puts on professional pilots, I strongly believe the Authority should abandon this regime and continue to rely on the interpretive skills of the AMEs. Life's tough enough without waiting two weeks to find out whether one still has the wherewithall to earn a living.
I'm old enough to remember the time when the CAA Medical Division ended up with serious egg on its face over ecgs and had to admit the limitations of these tests. I do have tremendous respect for the Aviation Medicine fraternity and I hope that they will take a pragmatic view and pull the plug on this "advance" sooner, rather than later.