NASA is reporting that the left gear was deployed and locked just before the breakup. This doesn't really mean much, since it only confirms problems on the left wing.

It's much more likely that this was a symptom of a problem (the wing falling apart from the inside from all of the heat) rather than a cause, but I've no doubt that tin-foil-hat afficianados will be claiming that someone sabatoged the mission by deliberately deploying the gear. That is nonsense on many levels, least of which is that it's not possible (as far as I know) nor would it be sensible to be able to drop the gear on one side only.

MSNBC reports that while a sensor reported the left gear down, two others in the same compartment reported it up.

From

LANDING GEAR THEORY DISMISSED
The board dismissed suggestions Columbia?s left landing gear was improperly lowered as it raced through Earth?s atmosphere at more than 12,000 miles per hour. NASA disclosed earlier Thursday that a sensor indicated the gear was down just 26 seconds before Columbia?s destruction.

[...]

Officials said they were confident that unusual sensor reading was wrong. Tires are supposed to remain raised until the shuttle is about 200 feet over the runway and flying 345 miles per hour.
Two other sensors in the same wheel compartment indicated the gear was still properly raised, they said.