Applying for masters again, will the application be evaluated on the basis of undergraduate/Bachelors or the most recent postgraduate grades
The admission committee will see your entire record.  It is up to them to decide how to consider and weigh the various parts of it - different people will feel differently about this, and there is no way to know what the sense of the committee as a whole will be.

If you had special circumstances that affected your grades, you should address them in your statement of purpose or cover letter.

See also:

How do you get a bad transcript past Ph.D. admissions?

Should I mention a &quot;math depression&quot; I went through in my letter of motivation?

Applying for PhD after a poor master&#39;s