My DVD drive is currently broken, so I cannot reproduce this issue at the moment. However, similar reports have been made in the past and we still do not know a definite solution. It seems likely that this behavior is caused by Windows rather than WinMerge itself.
Problems comparing DVD content vs hard disk
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This can already be achieved using existing features. In the Options window, go to Compare → Folder, set Compare method to Existence, and set Additional comparison condition to: abs(LeftSize - RightSize) < 1KB With this setting, files whose size difference is below the threshold will be treated as identical (see attached screenshots). As an alternative workaround, although it may be slower, you can use Tools → Customize Columns…, add Size via Additional Properties, and then enable Size (Diff) as...
PS: as a "cheap" workaround you can add a column type "size difference" and make it sortable
threshold for size difference