Yes, the field order will be different depending on the order of actions you take within the program. Also, Mp3tag's field mappings will affect the order. In files with VorbisComments, DATE and TRACKNUMBER are always last because (I assume) they're remapped internally.
To see the comments and the order that they're in, maybe the best tool to use is metaflac:
metaflac --list --block-type=VORBIS_COMMENT {some_flac_file}
I've found that if you're really concerned (or impossibly anal) that it is possible to get the VorbisComment fields written to the file in the same order every time. Someone else was asking about it here in the forums a while back and I was curious about whether or not it was possible.
First, you copy existing fields into fields with temporary field names (ARTIST to ARTISTX, for example). Make sure that you account for any fields where there may be multiple fields of the same name (using $meta_sep()). You also have to make sure that you handle all possible fields that may be present in the file, or else use a 'Remove fields except' action. Then delete the original fields. Then copy the temporary fields back again to the original field names in the desired order. Finally, delete the temporary field names.
You can create one (giant) Action Group to do this. If executed last among your actions it will result in always having the fields in the same order. The action group would look something like when viewed in Mp3tag:
Format value "ARTISTX": $meta_sep(artist,|)
Format value "ARTISTSORTX": $meta_sep(artistsort,|)
Format value "TITLE": $meta_sep(title,|)
Format value "TITLESORTX": $meta_sep(titlesort,|)
...
Format value "REPLAYGAIN_TRACK_GAINX": %replaygain_track_gain%
Format value "REPLAYGAIN_TRACK_PEAKX": %replaygain_track_peak%
Remove fields "ARTIST;ARTISTSORT;...REPLAYGAIN_TRACK_GAIN;REPLAYGAIN_TRACK_PEAK"
Format value "ARTIST": %artistx%
Split field by separator "ARTIST": "|"
Format value "ARTISTSORT": %artistsortx%
Split field by separator "ARTISTSORT": "|"
Format value "TITLE": %titlex%
Split field by separator "TITLE": "|"
Format value "TITLESORT": %titlesortx%
Split field by separator "TITLESORT": "|"
...
Format value "REPLAYGAIN_TRACK_GAIN": %replaygain_track_gainx%
Format value "REPLAYGAIN_TRACK_PEAK": %replaygain_track_peakx%
Remove fields "ARTISTX;ARTISTSORTX;...REPLAYGAIN_TRACK_GAINX;REPLAYGAIN_TRACK_PEAKX"