Hello,
Did you use Excel or another spreadsheet program open and save the TMY3 file? Spreadsheet programs may add commas to rows or change number formatting in a way that causes the files to be unreadable in SAM.
Please try opening your TMY3 file with a text editor and comparing it with one of the standard TMY3 files in SAM's weather file collection, and check the headers and date values to see if they look similar. Sometimes a missing value in a header field can cause problems. For example, no value for the state field, might cause problems.
As for running SAM on Linux with Wine, I know some people have tried it with some success, but I don't have any experience with it. Perhaps someone else does, and can share their experience here.
Best regards,
Paul.