I have used PIC chips to monitor pulses from an encoder but I made sure that I was clocking much faster than my fastest pulse rate. Obviously one needs to know quite a bit about the specific application and you have not yet given that kind of detailed information.
You may need to perform some tests and measurements to determine your maximum encoder rate. A PIC running on a 2MHz clock will have lots of time to execute as much as 100 instructions for an encoder that only produces 10,000 pulses per second. In that case, an interrupt approach is fairly easy and repeatable since it only takes a fixed amount of time to respond to the change of state. If you are polling and doing other things in between, the response can become a little jittery.
Perhaps you will describe the technical specifics a little more?
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A great troubleshooting tip...."When you eliminate the impossible, whatever remains, however improbable, must be the truth." Sir Arthur Conan Doyle