I am doing an integrated BS-MS in Biological Science from an Indian university and currently am in the 6th (post-final!) year. In this MS part of the program, I am supposed to take a few grad level classes and mainly focus in research. I also need to pass 8 MS thesis courses (worth 3 credits each), in which my supervisor grades me on my research work that particular semester (I can take as many as 4 of them in one semester). The grade for this course is either S or X i.e. Satisfactory or Fail.
I took one of the 8 courses in the summer following my senior year. I worked very little and met my supervisor only 3 times in the term. As a result, I received the X grade in the thesis course. In the following semester (Fall), I took 3 MS thesis courses. My performance was better, I met him more often but according to him, it was not worth passing all 3 - he said it was only good enough to pass 1 of the 3 thesis courses. But since failing 3 thesis courses would have led to termination of my degree, he gave me pass grade for 2 of the 3 courses and cautioned me that another fail course would mean the end of the program for me.
After this, my performance research-wise has been good, I have been more regular. My relationship with my supervisor has also improved, although it could be much better. I have received a pass grade in all the remaining thesis courses and retook the 2 I had failed. Since I had not made enough progress in the one year, I continued my work further until it reaches a publishable position. I am finishing my second year this summer (6th year overall) and the work seems to be coming to an end.
I applied to for PhD positions at US universities last fall. When I asked my supervisor for recommendation, he said - "Ya, I will write one for you, but it won't be a glorious recommendation. I will mention what you did, your performance in my course...". Anyway, the results came out, and it was not good (1 accept out of 9).
(hope this was enough of a background!)
My question is - How much does an X grade in thesis research course (2 such, in my case) affect my PhD application. Are these thesis credits looked at closely? Such X grades are rare in my department, so I don't know how bad the situation is.
EDIT - I think this question is sufficiently different from others asking about a failed subject course. I am asking about failing thesis credits, which is different because a) these can be easily retaken and one can take as many as 4 of them in a semester and b) they directly corroborate with your research performance as opposed to normal courses.
I would be SINCERELY OBLIGED if someone could help me with this. It has been troubling me for months, and any answer towards this question/situation would be enormous for me!