Regarding your corrupt file, check its properties and see if it reads 0 bytes.
If it does you are going to need some kind of data recovery prog to retrieve the data. If you havn't been using your system too much, you might be able to restore your file.
I get bizarre stuff like this on my win98se when BSOD problems crop up in the middle of processing a large file. The file is still there but is good for shit because it has no data.
I use messer for the stuff you are trying but you could look at this too.
http://www.1oo-percent.de/lamer/It allows you to encode with alot more command line control than messer but it may not have a timer. There have been a couple of new releases since I have used it, and the developer had said he was going to add a timer at some point.
Does the idea of compressing directly to high bitrate mp3 present a problem for you? High bitrate CBR is really easy to edit and would increase your possible recording time alot.