Is there anyway to standardize the tones on words (or are they already standardized?) It seems some are entered using the change rules, while some are not. For example, maybe there are two double character words ...the first one is in the system as 3-3 and the other might be in there as 2-3.

I may be mistaken... I don't know! Has any one else noticed this?

None of the third tone sandhis should represented explicitly in the system, but all of the tone sandhis for 一 and 不 are. If you find one that's wrong or inconsistent, report it as a correction using the feedback tab at the lower right of the study page.

On a related note, I've recently come across a couple of words where the pinyin prompt says it ends with a fourth tone, but the sound file definitely sounds to me like it's being pronounced as a first tone. The words I'm thinking of are:

痕迹 hen2ji4 or hen2ji1?

宝莱坞 bao3lai2wu4 or bao3lai2wu1?

痕迹 goes both ways. It is pronounced hén jī in Taiwan, and hénjì on the Mainland.

With the neutral tone for the second half of words, I've found that in some cases skritter accepts neutral or the character's tone, but in others does not. Which is correct?
For example 里面 only accepts li3mian5 - would nobody understand if I said li3mian4?

edit: in contrast, 右面 will only accept you4mian4 not you4mian5 - can anyone explain or is this an error?