The source end points should be recorded in as high a quality as possible with a high SNR. STRAIGHT scales the amplitudes, so if your stimuli were recorded with a lower gain, some noise might be introduced from the microphone, leading to artifacts in the eventual synthesis.
Additionally, the recording environment should not have noise in the background. STRAIGHT can remove some low frequency hums, but any noise in the frequency range of speech is going to be analyzed as speech and resynthesized.
The two end points that you’re generating a continuum for should be maximally similar, except in the one way you want the continuum along. So for a continuum from “bet” to “bat”, the /b/ and /t/ should be pronounced as identically as possible. In English, /b/ can be realized (albeit uncommonly) with prevoicing, and coda /t/ can be realized in a variety of different ways: released, unreleased, glottalized released, or glottal stop. If the two end points have different realizations, generating a continuum is much trickier (you can look at using bet_creaky.wav and bat.wav as the end points). In this case, I would recommend re-recording the end points to be more similar. Side-by-side productions can be used to elicit more similar pronunciations, as well as coaching the speaker about releasing all stops, for instance.
I would also recommend consistent modal voice quality, since pitch tracking is generally easier.
I’ve run into a random error that sometimes pops up on some versions of the Matlab code, where it will give a message about different dimensions of matrices. The fastest solution I’ve found is to redo the anchoring completely, and then run the continuum again and it should work. I think this is only relevant to the batch script that I’ve wrote here, I don’t think I’ve encountered the bug in the standalone versions.