¯K> What could go wrong here?
¯K> The main code is running in an loop polling the STAT,0 bit.
¯K> When it gets set the math is performed and the STAT,0 is cleared
¯K> again, and it goes back in the polling loop.

¯K> The TIMER_STR:2 variable is the count value used in the math.

You might want to try double-buffering of the 16bit timer.  If your math
takes a lot of time, and you're working on the same registers all the time,
you may get a new interrupt overwriting you previous values with new ones
while still not finished calculation with the previous ones.
This could work:

ISR routine:
    ...
    RETFIE

Polling loop
    pollwaitpollwait
    optionally-do-math
    keeponwaiting

Math
    GIE=off
    Copy TIMER_STR:2
    STAT,0=0               ; Do this early so you still register
                           ; interrupts while calc'ing.
    GIE=on
    Perform math on TIMER_STR:2 copies

The GIE should be switched off so your TIMER_STR:2 is not updated by the
ISR while you copy it.

rgds,
Dag S
Any programming language is at its best before it is implemented and used.