I seem to be getting different oscillation frequencies for a stellar model depending on whether I use an FGONG file or an AMDL file, converted using either ADIPLS' internal fgong converter (if you have MESA, it's at $MESA_DIR/adipls/adipack.c/adiajobs/fgong-amdl.d.f) or my own Python-based converter (using TOMSO). I've attached example files for Model S, with the AMDL file gzipped because otherwise it was rejected as an attachment.
For the summary using the FGONG model, I get
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1 2 3 4 5 6
l n_pg n_p n_g Re(freq) Im(freq)
0 21 21 0 0.3038081409866325E+004 0.0000000000000000E+000
0 22 22 0 0.3174111887772760E+004 0.0000000000000000E+000
0 23 23 0 0.3310180199798498E+004 0.0000000000000000E+000
0 24 24 0 0.3446893236132409E+004 0.0000000000000000E+000
0 25 25 0 0.3583918263283139E+004 0.0000000000000000E+000
0 26 26 0 0.3721163831988589E+004 0.0000000000000000E+000
0 27 27 0 0.3858790528140903E+004 0.0000000000000000E+000
0 28 28 0 0.3996454584650650E+004 0.0000000000000000E+000
0 29 29 0 0.4134355457053003E+004 0.0000000000000000E+000
0 30 30 0 0.4272334189292133E+004 0.0000000000000000E+000
0 31 31 0 0.4410314077774772E+004 0.0000000000000000E+000
0 32 32 0 0.4548466828006668E+004 0.0000000000000000E+000
0 33 33 0 0.4686358934199711E+004 0.0000000000000000E+000
0 34 34 0 0.4824085736439642E+004 0.0000000000000000E+000
0 35 35 0 0.4961514516938695E+004 0.0000000000000000E+000
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1 2 3 4 5 6
l n_pg n_p n_g Re(freq) Im(freq)
0 15 15 0 0.3102764484173943E+004 0.0000000000000000E+000
0 16 16 0 0.3290559811239307E+004 0.0000000000000000E+000
0 17 17 0 0.3479404763661229E+004 0.0000000000000000E+000
0 18 18 0 0.3669127390608365E+004 0.0000000000000000E+000
0 19 19 0 0.3859486183176797E+004 0.0000000000000000E+000
0 20 20 0 0.4050645670093928E+004 0.0000000000000000E+000
0 21 21 0 0.4242285556617217E+004 0.0000000000000000E+000
0 22 22 0 0.4434049354298812E+004 0.0000000000000000E+000
0 23 23 0 0.4625786127087709E+004 0.0000000000000000E+000
0 24 24 0 0.4817157007065860E+004 0.0000000000000000E+000
I started looking into the GYRE's source (and comparing it with the source for ADIPLS's FGONG to AMDL script) but nothing has jumped out at me as being incorrect. I'll keep digging, though.
Cheers,
Warrick