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I've been seeing this several times with different students with multi-sim. Simple circuit does not run, but simply replacing component with itself (like LED's) fixes it every time. Just last night we had a circuit that appeared fine, but replacing a 7447N with itself fixed it.
That sounds really strange, the only thing I can think of is that the students are opening a file created with the previos version and if there is a problem in the old file, you will see it in the current version and that's because everything was saved in the file.
