This sounds like maybe a default failure of X-Plane is invoked that makes the gear "stuck"? There is no failure coded into the IXEG 737 that will make a single gear not extend - if you fail the A hydraulics (either through the failure menu or by simply not turning on the pumps) the gear will not extend, but the manual gear extension will drop it.
I don´t have the QRH in front of my, but going by memory pulling the manual gear extension handle on the cockpit floor will ONLY manually release the uplock hooks (they hold the gear in the up position). But if you still have hydraulic power holding the gear up, it will not extend. So if the gear lever is in UP and A pressure is available, releasing the uplocks will not do anything.
There are certain failures (like the gear handle being stuck in the UP position) that trap A pressure, so to bring the gear down you have to release the pressure by first depressurizing the A system by turning off the pumps and THEN cycling certain A hydraulic users, for example the speedbrakes.
Cheers, Jan