Hi there,
You've had issues earlier where you had troubles before an upgrade or similar? Since this is continuing, would you want a proper sit down meeting with advisors, supervisor or any grad pastoral person to talk through issues? These things do not die a natural death, and if you are feeling your research has serious issues, or you are struggling and getting signs that you may not be able to handle the whole of it, on time, perhaps now is when you sit and deal with it with the folk concerned?
PS: Your name on this forum, I presume, has 'fire' in its first word 'Agni' and hence I think you should be strong!