First the basic quesiton:
Used my shiny new Edirol R-09HR for the first time last night, had to use the internal mic whilst awating external's to arrive..
It was quite a smallish venue & recorded in 48khz sample rate & 24nit wav & had the recording levels set to 28 - limiter, low cut & plug in power on the back set to off & mic gain set to lowbut certain parts of the recording seem quite bassy - is this likely to be down to the internal mic ? No sign of the sound affecting the "peak"..
I've read alot on here about "unity gain" but after reading various threads i'm still not sure what it is and how i alter it (if indeed it needs altering)..
I could post a sample ?
What you're hearing (and since you already bought external mics, I don't feel bad telling you this) is that the internal mics are garbage. Also, a lot of live recordings tend to be bassy anyway.
Unity gain is what people talk about when using external preamps- basically the point on the volume control when using line-in where the recorder is not adding or decreasing the gain (i.e., the recorder's role is "neutral" and the gain is controlled by the external preamp). On the R-09HR it's believed to be at 40, I think. Unless you're using an external pre on line-in, though, this is irrelevant.
As to your other issues, I'm not sure. The clicking could be an issue with the SD card you're using, or it could just be distortion from the mics being overloaded, though the way you describe it, it does not sound like that. You may want to post a sample and/or a pic of the waveform.
Also, as long as you're using the internals on that unit, you may want to save some card space and just use 16bit. I don't think sonically it'll make any difference. Just IMO.