I usually have to program "dummy" channels on the lower and upper end of the tuners bandwidth to keep it aligned.
Like if my control channel is 853mhz, I'll put a dummy NBFM channel at 848mhz and another at 858mhz, then I'll have them start sequentially so it'll lock on CC, shift to cover lower end dummy channel, then shift again to the upper end, thus locking it in position.
update: I forgot that recent versions of SDRTrunk have a MIN /MAX frequency in the tuner menu, this will achieve the same results.