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Nothing to do with the state of Windows.
The dirty bit in NTFS is set whenever file handles are openned for write access. It is turned off when the handles are closed gracefully.
Obviously if the system crashes or something happens to the disk, the bit is left set and it needs a file system check to reset it. Because the Linux handling was reverse engineered, the linux NTFS drivers cannot be sure that they can reset it correctly so it has to refuse to possibly complicate an error - quite correctly. It is also why some Linux NtFS drivers will refuse to write - because they cannot be sure that the error correction is correct.
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