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Fiber optic Fabry-Perot sensors are commonly interrogated by spectral interferometric measurement of optical path difference (OPD). Spurious jumps in sensor output, previously attributed to noise, are often observed in OPD-based measurements. Through analysis and experimentation based on intrinsic Fabry-Perot interferometric (IFPI) sensors, we show that these discontinuities are actually caused by a time-varying interferogram phase term. We identify several physical causes for varying initial phase and derive a threshold value at which it begins to cause errors in the sensor output. Finally, we present a total phase measurement method as an alternative to OPD-based techniques to reduce the occurrence of output signal jumps.