I'm testing my software now using an infinate loop which is only left on the PCA interrupt. Every time I got my second capture I disable the PCA Interrupt (IE.6 = 0), process the values and enable the PCA interrupt again.
The first readout is fine. Then the microcontroller hangs or resets. To me it seems that the PCA int isn't disabled. I've checked this in a simulator and it seems to be enabling / disabling
Probably your ISR is too long/slow.
A non-disabled interrupt as an error source as well as too long/slow an ISR would show in the ISR reentering itself and pushing the stack.

One way to check would be to do the following at the reenable:

EA = 0
ISRint =1
EA =1
RETI

this would ensure that you never call the ISR from the ISR since EA=1 and RETI are protected from interruption.

Erik