MainConcept H.264 frame rate issues with Final Cut output

Hello, first time poster hoping the vast knowledge here can point me in the right direction :)

I am using MainConcept Reference to encode a file output from Final Cut using its QuickTime Exporter (It's a friend's file). The frame rate on the input file is showing "Variable", with the lowest fps at .003 and the highest at 29.97 for an overall framerate of 0.978 fps. MediaInfo says the video portion is ~5min but the audio portion says it's 10sec (which it should be).

This file plays perfectly in QuickTime, but when I encode it with MainConcept to H.264/AAC, it comes out as a 5min file with the video slowed waaaay down. If I take the file into QuickTime Pro and re-export with the same settings (essentially washing the file I guess), then use that file in MainConcept, it encodes perfectly.

I have tried all variations in the H.264 codec settings and have been unable to get the frame rate to come out right. Has anyone experienced a similar issue, or know of a way to get MainConcept Reference to handle Variable frame rate inputs?

Here is the MediaInfo output of the source file from FinalCut (pre MainConcept Reference)


Format : MPEG-4
Format profile : QuickTime
Codec ID : qt
File size : 32.7 MiB
Duration : 5mn 15s
Overall bit rate : 870 Kbps
Encoded date : UTC 2009-10-07 02:52:37
Tagged date : UTC 2009-10-07 02:52:39
Writing library : Apple QuickTime

Video
ID : 2
Format : AVC
Format/Info : Advanced Video Codec
Format profile : Main@L4.1
Format settings, CABAC : No
Format settings, ReFrames : 2 frames
Codec ID : avc1
Codec ID/Info : Advanced Video Coding
Duration : 5mn 15s
Bit rate mode : Variable
Bit rate : 820 Kbps
Width : 1 440 pixels
Height : 1 080 pixels
Display aspect ratio : 16:9
Original display aspect ratio : 4:3
Frame rate mode : Variable
Frame rate : 0.978 fps
Minimum frame rate : 0.003 fps
Maximum frame rate : 29.970 fps
Resolution : 24 bits
Colorimetry : 4:2:0
Scan type : Progressive
Bits/(Pixel*Frame) : 0.539
Stream size : 30.8 MiB (94%)
Language : English
Encoded date : UTC 2009-10-07 02:52:36
Tagged date : UTC 2009-10-07 02:52:39
Color primaries : BT.709-5, BT.1361, IEC 61966-2-4, SMPTE RP177
Transfer characteristics : BT.709-5, BT.1361
Matrix coefficients : BT.709-5, BT.1361, IEC 61966-2-4 709, SMPTE RP177

Audio
ID : 1
Format : PCM
Format settings, Endianness : Little
Format settings, Sign : Signed
Codec ID : sowt
Duration : 10s 276ms
Bit rate mode : Constant
Bit rate : 1 536 Kbps
Channel(s) : 2 channels
Sampling rate : 48.0 KHz
Resolution : 16 bits
Stream size : 1.88 MiB (6%)
Language : English
Encoded date : UTC 2009-10-07 02:52:36
Tagged date : UTC 2009-10-07 02:52:39