Can anyone explain the basic differences between running your script through WED or SED, and running it after it's been published?

My game works fine when I run through WED, but after publishing it, it crashes with no explanation.

I increased the warning level to 6 in WED, and it starts without any warnings, but it still won't start when I try the published version.

In the publishing process, it says it's skipping only one file, which is acknex.wdf. According to the manual this is only used by the professional version ... I have commercial.

I am still using A7 engine, if that makes a difference.

Any help would be appreciated.