Usually it is caused by wear and tear. If you have replace the shifter linkage [#202 in the above diagram] with new parts then I would say that you have been forcing shifter [#10] to shift gears rather heavily. The shifting fork can bind in the housing [#1] from corrosion. The spring and detent steel ball [#20 and #22] can rust up causing problems, Also where the steel detents in the shifting fork can wear heavily over time. Even the shift collar [#9] and keys [#8] can cause problems.
Either the Peerless transaxle has to be repaired or replaced with another used one if you can find one. They have been out production for quite some time.