If one - or more interrupts happened, you will get one interrupt; however the problem will be that the time you react to the interrupt will be wrong as the time to execute the 'undisturbed' instructions will be added in your calculation and thus the pulse count will be wrong also, if you use automatic reload, the next measurement will be wrong. Find a way to reduce/eliminate the code that must be protected from interrupts. Btw it it very bad practice to set and reset IE bits as you do, Push IE, clear the bit and when you are done pop IE.