So nobody can say the timescale that it 'should', in normal circumstancs, be paid in then?
Without JSPs to hand and only going from what is in my alcohol-addled brain (The morning after, the night before!) the 'normal' timescale is approx 6 to 8 weeks. That is assuming that all the right inputs went in at the right time, the det was actioned correctly onto JPA and no gremlin has screwed up the system. After the second pay run
sans allowance, the individual should put in an I-support detailing the nature of the problem with dates, location and the allowance that is reasonably expected to be received. If the I-support is closed or not resolved to your satisfaction, cut and paste the whole chain and re-iterate the problem. This alas, will probably take about another month.
If the second I-support is closed without resolution, then escalate the problem to your 1st RO (aka Section Commander, Flight Commander, WO, etc) with a print-off of what you have done to resolve the problem, so that they have sight of what could be a drama in your life. They will advise you to take it to the Unit HR (Sqn Clk) and then the Unit HR will have a go at batting for you. If they have no joy (which from the sounds of it , they won't) they will then advise you to take it to the SNCO PSF or Chf Clk, depending on who your Sqn Clk knows best (another month gone by now).
The SNCO PSF or Chf Clk will then take over the problem as you have done your best and the Sqn Clk has done theirs. (At all points, take print-outs with you as they can do nothing without evidence) and they should be able to resolve the problem in a week or two.
All in all 4 months for the worst problem should be the timescale. Personally, I know that the scribes in PSF are getting grief for problems that are not of their making and that Chf Clks are getting the same for not making sure that people jump through the hoops. They are trying to look after people and cut down the horrible length of time that it takes to resolve the harder than usual problems.