ATC in FS is crap...nothing more to say about that.
It was one of the things I asked to be improved in FSX, and is one reason I still use FS9.
Had the same weird issue when closing 4L-22R at JFK for landing.
When I did that neither 4L-22R or 4R-22L was used at all no matter what wind direction.
		
		
	 
There are many web sites that make comparisons of FS9 / FSX ATC and in some cases the posters do not have a good working knowledge of how MS coded certain areas of the simulator.
Rather then say ATC in FS is c*** there are many developers here that can explain the working code used by ATC and what it might take to get ATC to understand what you might want done. In certain cases you may not want to have runways closed or open independent of each other but ATC in FS also try's to use some basic real world logic. 
Runways in FS2002 (FS8), FS2004 (FS9) and FSX at some airports work identical. That does not mean one version of ATC does it better then the other but MS leaves certain runway code the same on purpose. 
Parallel runways in FS9 and FSX are paired into groups. In order to do this there is a lot of coded intelligence into the runway property's so FS can try and do the right things and not what the User might expect.        
When you closed runway 04L/22R for landing then it forced 04R/22L as a single landing runway since the 2 parallels are grouped together. FS2002 uses what I call the 1 ft. longer runway rule for landing. This same rule for KJFK runway 4 and 22's also applies in both FS9 and FSX (there is no difference per FS2002).
When you closed Runway 04L/22R for landing then 04R/22L by default was forced to be the landing runway and FS sent the runway property through a formula in FS9 and FSX which looks like the following.
Score = 0
If runway length > 70% of longest runway at airport -> Score += 50
Score += tailwind or headwind (tailwind < 0 and headwind > 0)
If (unknown 'runway group' flag) Score += 10
Score -= crosswind <<<<<<<<------------------------------------ add 100 points if my CW technique is in use
If (runway landing==yes) -> Score += 100
If (runway takeoff==yes) -> Score += 100
calculated score for the runway gets multiplied by 10000
Any Jet type aircraft defined in the aircraft.air file uses a Empty Weight (EW) vs runway length that says
If no empty weights specified in the .cfg: returns 5000ft
Else:
value = ((empty_weight pounds - 10000) * 2000 / 90000 ) + 5000
if ( value > 7000 ) return 7000
if ( value < 5000 ) return 5000
else return value based on EW vs runway length 
In User terms all the above formula's mean, when runway 04R/22L became a forced landing runway for all arrivals FS looked at the overall runways and recalculated to say the 13/31 runways are a better choice for takeoff and landing. This removed the use of both 04/22 runways from the total runway grouping. The 04/22 runways at KJFK are the secondary crosswind runways as defined by real world runway percent usage on a yearly basis that considers prevailing winds. The 13/31 runways are the primary usage runways per data compiled by the Airport Authority. FS also imposes this same set of compiled data when calculating active runway usage at many airports in the FS database.  
I have no idea what your aircraft.cfg EW's are for all your AI Planes. Most AI FD developers do not know that these type weights have a big impact on runway selection when you the User try to force runway closures.
My EW settings in the aircraft.cfg are correct as per Reggie Fields and Martin Gossman's work here at FSdeveloper. Martin also has the owl's nest web site and utility for reworking develpers AI plane cfg files (also added into the ADE installer).
We here at Fsdeveloper would rather have users ask can something be done then then say ATC is c*** since this misleads many new comers to the ADE forum.  
Both my FS9 and FSX KJFK use runway 04L for takeoff and a forced 04R for landing when winds are light and varaible as per the rules that MS applies to the EW, runway length and some additional coding left over from FS2002 (1 ft. rule).
FS9 4L Departure. All winds are light and varaible at 8 kts and a 043 wind heading. 
 
FS9 4R Arrival
 
FSX 4L Departure
 
FSX 4R Arrival
 
My 4L/22R is closed for landing. My 4R/22L is not closed for anything since FS cannot calculate that runway as a departure runway based on Main Terminal position.