how to avoid to being blamed of self-plagiarism in this case? We have the following "weird" situation in the institution that I am currently working on. We have a master´s degree in CS that requires that the students present a thesis or a research article so that ourinstitution could grant them their MSc title. The background of the situation is the following:

a) Some students had published an article or had an acceptance letter, from a conference or journal, related to their MSc research. This situation has occurred, in some cases, just when they had finished the compulsory courses.

b) It is required from our institution that all the master´s students must present a public dissertation of their research work, this is commendatory to do it for grant them the MSc title. After this dissertation, the student should submit their research work, article o thesis, to be stored in the public repository of our institution.

The problem that we are facing now is how to avoid that one student who had his research work, accepted or published, before it has been put on our institutional repository or vice versa to be blamed of self-plagiarism. For example:

A student X has decided to submit its research work when he is about or just finished his master´s courses. The publication get accepted so it appears in the web page of the conference or journal in which he has submitted his work. This student X need to make the public dissertation and put his paper on our institutional repository, in this part we see two probable outcomes:

a) Somebody could blame the student that he has put, in our repository, a research work that has already been submitted; so it is a case of self-plagiarism.

b) Let´s suppose that the journal or the conference proceedings suffer from a delay, which usually happens when the proceedings are published by a third party, so this student X makes his public dissertation and his research work is put on our public repository. Then one person from the conference or journal could say that this person has made self-plagiarism because the work has already been published in another repository.

How to deal with this situation?

Thanks
There are two issues here. One is self plagiarism as the term is commonly used and there is what a University will accept for any course or degree work. The latter can be stricter than the usual rules because the goals are more nuanced, involving the student's education, not just the validity of the work. 

I doubt that this can be considered self plagiarism, provided that what was submitted to both places is the same. Keep in mind that the purpose of self plagiarism is that a reader needs to be able to see the entire context of a work in order to judge it and to extend it. If people just copy without citation from their own work it breaks the chain of reference that scholars require. But publishing the same work in different venues doesn't do that. Each work is complete. And when copying does occur, citation avoids any claim of self plagiarism, since the thread of context is maintained. 

But, given that, the student may still not be meeting university requirements, in particular if there is a rule that submitted work not be previously published. If this is the real nature of the problem, then you need to find a local solution, since we can't advise on rules we haven't seen and have no ability to enforce or not. 



Multiple publication of the same work might run afoul of copyright rules, but I don't see a hint of that in this case. And multiple publication does occur as when old papers are put into collections. This can be valid or not. But it isn't plagiarism or self plagiarism.