They're 0-based so Index 00 is the first track at 00:00:00 and then Index 01 starts at track #2. But I think your issue is that it looks like your actual track is in its own file. Changing the cue file only works this way if you have the entire album as a single flac file as then the cue file is how MC knows where the track boundaries are. If each track is its own separate flac file, then updating the cue has no effect as MC isn't using it to determine which tracks are which, it just plays the single file.
All tracks start with INDEX 01 ... INDEX 00 is pregap ... while higher INDEX are like chapter (feature that is rarely used in CDs)
I used to rip in one large flac with CUE (seems like best way to ensure bitperfect) .. but then change all ripping to tracks with new corresponding CUE (better compatibility ... while combining separate tracks with CUEtools into single large file yields same bitperfect large file)
I think MC uses CUE even if that CUE points to multiple tracks (any changes i make to CUE are detected by MC)
I made some test with
INDEX 00 00:00:00
INDEX 01 02:14:00
Loaded CUE into VLC and foobar
foobar: starts track at 2:14:00 ... progress bar starts at 2:14:00 ... so there is no way to play pregap
VLC: starts track at 2:14:00 ... progress bar starts at 0:00:00 ... so if one wish - one can rewind to listen to pregap
Obviously ... i prefer VLC way
So its eigher VLC/foobar got it wrong ... or MC got it wrong
PS. [play range] in MC works ... but CUE "solution" is "universal" in that it works across other players