Hi, welcome to sevenforums.
Indexing can take a little time, however 2 things to note.
Indexing should not run at boot time and shouldn't be rebuilding the index unless you specifically tell the program to.
Indexing on 300, 000 files should not take anything like the time you suggest.
I don't know why you suspect indexing as the primary cause of this problem. Have you done malware and rootkit scans recently ?