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Windows movie maker is a utility Microsoft included with Windows as a way for one to create video clips to share or publish. However, like its other utilities (Wordpad, Mspaint, etc.), it is very limited on features and is possibly not importing your recordings properly.
Have you tried processing or merging your recordings using another utiltiy, e.g. VirtualDub, AviDeMux, etc.?
If you made your recordings in MPEG2, the utility MPG2Cut2 does a pretty good job at splitting and joining clips without the need to re-encode them. However, if you need to convert the final edited version to another format, you can use pretty much any video encoder that accepts MPEG2 as input.