Among the many changes introduced with PeakTrace 6 was an improvement in the PeakTrace basecalling. This has resulted in some bases that had previously been called as Q6 now being called as Q5. Since these bases are unlikely to be useful (a Q5 base is expected to be wrong about 32% of the time, while an Q6 base is expected to be wrong 25% of the time), this change is of minor importance except that it can cause an issue if you are using a very old version of Auto PeakTrace RP (pre-5.70) and have the N base threshold set to 0. If you are you will now see some N bases in your basecall.
If this is an issue for you the best solution is to upgrade to Auto PeakTrace 6 RP since there are a number of new features that can’t be accessed using old versions of Auto PeakTrace RP, however, you can work around this change by setting the N base threshold to 1 rather than 0.