There is a continuing need for improved analytical techniques to measure the concentration of trace gases for monitoring hazardous air pollutants, industrial emissions, chemical-warfare agent release, etc. Methods of analysis that can conclusively identify several analytes in a mixture are particularly desired. Towards this end, the use of Fourier-transform microwave (FTMW) spectroscopy as a quantitative analytical technique has been proposed. The high spectral resolution of FTMW provides a quick and unambiguous method for identifying multiple analytes in the gas phase. A small-scale FTMW spectrometer has recently been constructed for use in quantitative analysis. Prior to the present investigation, however, the use of this spectrometer in quantitative work has not been rigorously evaluated. This work summarizes efforts to identify and categorize sources of signal instability in the FTMW spectrometer. Methods employed to minimize these effects will also be discussed.