They could also be using a different system with a different (possibly higher) threshold for positive vs negative than what the sending facility uses. The "in-house" system we use is fast but it requires a fairly high load before it give a positive result. The system we use for our "send-out" testing, which has a 24 hour turnaround, is far more sensitive but it does take that 24 hours. We used to use a 4 hour TAT system, but apparently no longer. So, we're at a 45 min TAT or a 24 hour TAT...The second PCR was probably collected with poor technique in this situation. That is definitely a positive. Why the hell did the receiving waste a test when there was a positive in the system?
Now that being said, we have probably seen more COVID+ patients using our 45m TAT system in the past week than we've seen in the month or so before that. We'd see 1-3 patients per day, most tested neg. Now we're seeing more like 8-10 and about half or so are pos.