Hey Tom,
looks like an error in the Level D format. I just compared the CRJ-200 dataset vs any of the Airbus X ones (all the airliners from Flight Factor, JARDesign, Rotate seem to use it) or the GNS430 one (same format?).
I'm also using NavDataPro and checked both the latest and an older set from 2014. The Level D format has the wrong altitude no matter what.
Airbus X Format:
FINAL,I26,26,I,3
IF,COD79,51.88496389,11.62938056,ICOW,75.0,9.0,1,3000,0,0,0,0,0,0
CF,OM26,51.87275000,11.54009444,0,ICOW,75.0,5.6,255,3.40,1,1930,0,0,0,0,2,0
CF,RW26,51.85837500,11.43570556,0,ICOW,74.9,1.6,255,4.00,1,646,0,0,0,0,3,0
CA,0,255,2,2000,0,0,0,0,0,0
DF,MAG,51.99498889,11.79430556,2, ,0.0,0.0,1,4000,0,0,0,0,0,0
Level D (OM26 only):
<Name>OM26</Name>
<Type>Normal</Type>
<Latitude>51.872750</Latitude>
<Longitude>11.540094</Longitude>
<Speed></Speed>
<Altitude>3000</Altitude>
<AltitudeCons></AltitudeCons>
<AltitudeRestriction>at</AltitudeRestriction>
<Flytype>Fly-by</Flytype>
<BankLimit>25</BankLimit>
<Sp_Turn>Auto</Sp_Turn>
Bonus screenshot.