cmlover,
IMO, there is perhaps a couple of fundamental problems with some basic assumptions you are making that is leading you to premature, incorrect conclusions (or raise questions implying such conclusions):
1. You are assuming that all frequency components you are seeing is exactly there in the vocal part of the signal (the only part you are interested in) when in truth there are many factors that can prove this otherwise: Polyphony - as in mridangam, tampura, violin; Noise (even if our ears can filter this out, they can be at a level that can show up significantly on spectrograms); Limitations of FFT itself
2. To know something is "off shruthi" one must understand how the gamakas appear as pitch curves in FFT. You started off with the assumption that FFT can show minor shruthi slips that the ears can miss, and more importantly any variation that "doesnt look right" is really there and is a miss. Now, FFT will show minor pitch variations that most (if not all) human ears can miss, because of #1 above it can show wild variations which most musically trained ears will catch. Before one can label what is a shruthi slip or not, one must be very clear on two things:
a) what is the pitch curve expected? Note that there is no single exact curve for a gamaka (arvindh shows this and it is definitely true). So what the expected set of curves (or general shapes).
b) Is the FFT result reliable for that particular signal at that particular spot? Does it have noise components? Was it thrown off by polyphony, consonant starts and attack phases?
Of course there can be variations which are beyond the threshold of normal/average human hearing - i.e. natural tremolo of the human vocal chord. Note also that for male voices in mandra stayi if the voice goes a bit "kara-kara", the harmonic nature comes down a lot, and once again FFT can get quite confused and show all sorts of junk. The reason you would find flute better is because it is higher pitched and a very harmonic sound. Female voices can be better. Male voices are hit and miss. This is just from my experience.
In any case, without knowing (a) and (b), it is not prudent to jump or even ask questions about "is it a shruthi slip". You/We should first ask
1. Did it sound proper to our ears?
2. Are we sure that the FFT results reliable for this particular signal at that particular time? (how much smearing is there? Is there interference from noise and other things? Are those interferences separatable?
3. What is the pitch curve - expected vs.shown?
I also think by the kind of conclusions you are leaning towards, vgv's comment makes a lot of sense. While I know where you are coming from (difference of opinions about shruthi lapses etc.), the kind of questions based on the FFT analysis of this signal alone (which I think is poor - i.e. signal not ideally dissected), vgv's counterpoint rings quite strongly true

So I suggest a different and more cautious approach.
Arun