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Thanks for the suggestion but now solved, although I infer that the problem is little to do with Latex!

The files I am trying to compile are on a server, some virtual thing on a (Linux) NAS box somewhere which exports SMB shares.

1) If I try to compile a (Bakoma/Windows-generated) file in situ on ...

I have a large collection of files, created using the commercial BakomaTeX package under Windows, which I would like to edit and process using TeX Live under Ubuntu 11.10. I have a fully working TeX Live 2011 installation.

When I try to open one of these BakomaTeX generated files in TexMaker on ...

Just to tidy things up: I have finally found the reason for this odd behaviour!!! It's caused by BakomaTex which inserts "%&latex" as the first line of a file. This produce the weird error above. Delete this extra line and it all works beautifully!

I came to this conclusion from downloading a copy of the bare journal tex file from the IEEE and adding small section of text. This worked fine with BakomaTex on Windows (which I believe uses DVI). When I tried to move to pdfLatex on Linux I got an output from Latexmk that said:

...
-- Using DVI ...

I am trying to use the IEEE document class IEEEtran with pdfLatex (via TexWorks) to produce PDF output. By default, IEEEtran specifies DVI output. The class documentation tells me that there is a CLASSINFO control, \ifCLASSINFOpdf that is set to false by default and controls pdf output. But the docs ...