My point with P3_1 is that even though it doesn't exist in your package, if the timer simply needs to be tied to a configured pin to work then that may help. Does your .h file include an entry for P3_1? Again, this would just be a workaround, and may not be possible, but the register exists to configure the pin even if it's not called out explicitly (since the existing P3 pins would be in the same register). Alternately, I may have misunderstood what you were doing with P1_1. Were you simply configuring it as a timer input and leaving it open (since the signal should be coming from a different source anyway)? Or were you feeding the signal to that physical pin as well?
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