You're posting in the Windows forum, so presumably you're running the windows version.
So why are are your path separators showing as / instead of as \ ??
That doesn't happen on my PC.
Also, I see this in your log:
0016641: 8304: Import: ImportNewFiles: Adding: C:\Users\Maarten de Wit\Music\Muse\2009 The Resistance\01 - Uprising.m4a
0016641: 8304: Import: JRAnalyzer::AddFile: Filename: C:\Users\Maarten de Wit\Music\Muse\2009 The Resistance\01 - Uprising.m4a
0016672: 8304: Import: ImportNewFiles: New File: C:/Users/Maarten de Wit/Music/Muse/2009 The Resistance/01 - Uprising.m4a
The song Resistance is being imported twice, but at two different paths, because the separator is / for one and \ for the other. If the same file can be found at two paths, MC is obliged to consider it two files, as it can't distinguish.
It is easy to achieve multiple paths to the same file on Linux, and it can be done on Windows with junctions or network shares. But seeing a mix of / and \ on Windows is odd.