It sounds to me a problem with a not configured oto.ini or the problem with resampler.exe and the decimal symbol being a comma.
oto.ini is a file that tells UTAU how to use properly the samples of your voicebank.
Let's say if your voicebank is a car, having no oto.ini is like that car using square wheels.
Check this thread
or this tutorial
for a starting guide on how to do it.
If oto.ini is not your problem and the problem appears even for other voicebanks with a good oto configured (you could check another one) it could be a problem with your resampler.exe not working properly.
The fix for that before was to change to resampler.dll and fight against how bad it renders some notes but it seems it was found a way to fix resampler.exe for those problems. Check this thread
for more info.
About programs to record your samples, if you want to re-record again... the classical options are Audacity or OREMO. Recently Reaper is getting some popularity, too.
There are tutorials for OREMO and Reaper in youtube. I can't find any for Audacity but we have here one in "Tutorial and Resources Directory". Just dig a bit there.
But to tell the truth any program may be good to save the samples. Even Microsoft sound recorder could do it, I guess.