If you record one track from zero to the end of the song, think of that as one wave file.
Because you can use Undo, every punch-in or overlapping recording you do on this track becomes a separate wave file in a new location.
Staying with the one track example, if you have several short punch-ins, when the machine plays back in real time it has to look ahead and read these files into the playback buffer. If you have many, many short recorded parts and drop-ins across 16 current virtual tracks you can see this can become quite complex. This is why you get the Disk Busy message - a further file call has been made but the machine is still busy performing the previous one. Normally it can cope with this. However, when it reaches a stage where it can't, you can not only get jerky playback but can sometimes hear the wrong parts in the wrong places. If this continues, you can actually get corrupted files and your song is ruined. You may also find that the machine does a spontaneous reboot.
You can check this before you hear it by going to Utilites and running a chkdsk (careful - NOT format) to see if you get any reported Link Errors. If you do, the song is on the way out. So, at your first Disk Busy message, you need to backup your song to disc and continue doing this often until the song is complete. A MERGE would also be in order.
You can reduce the number of calls in a track by doing a MERGE. This simply takes all of the files that make up one Virtual track and concatenates them into one continuous file, with silence in the spaces. You can see this, before and after, by going to the Track View screen. Where there may have been mutilple lines for a track with spaces in between, you will now get one continuous line. I think Yamaha introdcued the MERGE function after release to address this problem.
As for the drop-outs, are you are using auto punch? If so, there is a pre-roll time where you hear the original recording before the machine drops into record. In this pre-roll time, the red recording light blinks and it only goes solid once recording commences. You can alter this pre-roll time in Preferences but you can't make it zero.
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