yes, interesting... i also had strange issues trying to implement rtc first time, but it was due to arduino lib mucking with Timer2 registers (due to Tone libs). The answer was to make sure all registers were not assumed to be default, but explicitly set in setup(). You seem to have that here.
I did a quick scan of mysensors repo code, but I don't see where it is touching any of Timer2's registers, so not sure.
Did you toggle led/pin in the current code's ISR, to be 100% sure your the issue is that the isr is getting triggered at unexpected interval? (maybe sanity check that with scope.) That should bifurcate the problem either to the timer implementation/configuration, or something else.
@zboblamont I also agree here. But it should be totally possible to setup Timer1 as externally clocked counter, i.e. pulse from meter can increment Timer1 counters without interrupting CPU from sleep, and only interrupt and increment another counter variable on Timer1 overflow (if it happens) so you can be sure you have complete, accurate count when you wake up from your long sleep to do your accounting and reporting.
Briefly looking at the datasheet for the water sensor, I didn't get a sense of what the unit of water volume/flow a single HF pulse means. Depending on what this unit is, and how often you wakeup and check the T1 counter value, it may not even be necessary to bother with handling counter overflow, e.g. pulses = 1 liter; would you ever consume >65kL in <10 mins?
In this case, you only simply need to worry about waking up from long sleep interval, polling and clearing counter, sending, and going back to sleep.