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We are running a gel on the products of a restriction digest to determine the size of an insert. We know the vector backbone size should be ~2.9kb; however, the standard appears to be running too quickly (or our samples too slowly), causing the backbone size to be about 4kb (which distorts our results for the insert size).

What could possibly cause this? Thank you.

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Are the salt concentrations identical or similar in your sample and the standard? –  Mad Scientist Dec 5 '12 at 12:07
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Are you sure you have complete digest of the vector? –  bobthejoe Dec 5 '12 at 21:34
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If the salt content or pH is different than "normal," run time can be affected. After all, you're applying an electric current to the sample(s) and ion concentrations and pH are sensitive to that current. Of these two, salt/ion levels are more likely to have an effect as your samples/markers are likely to be adequately buffered.

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