Can you post pictures of the frqs so we can see if there's a problem with it or not? It usually is an erratic orange line or a sudden drop in it. And how low is low? Can you give an example?
Also about the sounding weird on low notes. Speech synthesis based resamplers usually have issues with pitching down notes and UTAU is no stranger to this. So, for example, if you record your bank at F4, if you try to use it at F3 or lower (depending on how the mic is recorded), it would generate a weird sound with the sample since it's going outside of its range (someone correct me if I'm wrong). The only way to fix this is to record extra pitches to allow the bank to go lower without creating extra noise.
Flags tend to work sometimes depending on the bank as well (Y, H, C and F are really good for helping with clarity and stuff) and sometimes help with that pitch probably. So, just play around with it and see how your bank works.
UTAU should give the logical range of your bank (its usually 6 semitones up and six semitones down from your recorded pitch. For example, a bank recorded at C3 usually has a logical range of D2 -> B3 or there about). You can find this out by clicking the icon at the top left (the utau you loaded) and it should give the logical range with the average frequency of the bank as well. This will help with keeping your bank within a range where it works well and not give errors.
I hope this helps.