Invalid VIDEOINFOHEADER2 before playback start

Question

I have a problem connecting Microsoft DTV-DVD Video Decoder to my filter. This usually happens with flv files. Here is how VIDEOINFOHEADER2 looks after connection and after play start (when first frames have passed):

Before play (after connection):

VIDEOINFOHEADER2:
          rcSource:             (0,0,544,368)
          rcTarget:             (0,0,544,368)
          dwBitRate:            71997051
          dwBitErrorRate:       0
          AvgTimePerFrame:      333667
          dwInterlaceFlags:     129
          dwCopyProtectFlags:   0
          dwPictAspectRatioX:   544
          dwPictAspectRatioY:   368
          dwControlFlags:       0

      BITMAPINFOHEADER:
          biSize:               40
          biWidth:              544
          biHeight:             368
          biPlanes:             1
          biBitCount:           12
          biCompression:        0x3231564E
          biSizeImage:          300288
          biXPelsPerMeter:      0
          biYPelsPerMeter:      0
          biClrUsed:            0
          biClrImportant:       0

During playback:

VIDEOINFOHEADER2:
          rcSource:             (0,0,540,360)
          rcTarget:             (0,0,540,360)
          dwBitRate:            0
          dwBitErrorRate:       0
          AvgTimePerFrame:      333667
          dwInterlaceFlags:     129
          dwCopyProtectFlags:   1
          dwPictAspectRatioX:   540
          dwPictAspectRatioY:   360
          dwControlFlags:       8321

      BITMAPINFOHEADER:
          biSize:               40
          biWidth:              768
          biHeight:             -360
          biPlanes:             1
          biBitCount:           12
          biCompression:        0x3231564E
          biSizeImage:          414720
          biXPelsPerMeter:      0
          biYPelsPerMeter:      0
          biClrUsed:            0
          biClrImportant:       0

As you can notice, there is difference in video size. This is really important parameter, especially when you want to do color conversions (like I do in my filter that is connected to Microsoft DVD-DTV decoder). Is there any way to overcome this? Thanks!