Two different length antennas can cause problems?
As Andvaka said, there are many things that could be affecting range.  For this to be properly answered, more information should be given.  Without this information, I am assuming you are using two quarter-wave monopole antennas.  Any change in length from the ideal quarter-wavelength length will, most likely, degrade the performance of the antenna.  In order to properly design these antennas, a network analyzer would be needed to tune the antenna for the given environment (most things within the near-field range of the antenna will affect its resonance frequency).  Without this equipment, I would design their lengths to be a quarter-wavelength in length.  Also, since this type of antenna works with a single-ended signal, you need to ensure that you are actually feeding the antenna with a single-ended signal and not a differential signal.  In addition to all this, make sure that the antenna are oriented so that there is no cross-polarization mismatch.  This essentially means that both antennas should be oriented in the same fashion, i.e., both vertical.  I hope this helps...