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Try this:
In the registry under HKey_Classes_Root you can create a key for the extension (ie .SHH) and create a "filetype" entry. (create a string value called "Default" and entry a filetype (is. SHHFile).
Then create a key called SHHFile" (or whatever your filetype was called) and create a Shell\Open\Command string value which has a Default string value that points to the executable file you need to open your file type.
Of course editing your registry is risky if you make a meal of it. So do a backup first. If you have never played in your registy before then I'd be inclined not to bother.
When you say that sometimes it will run it and sometimes it won't it's unlikely to be an association problem.
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