I have a fresh install of 4.1.2 on a HP-UX 11v3 box and it automatically paused indexing. I've moved the indexes over to a file system with plenty of free space, and after restarting, it failes to resume indexing.
There are many reasons why indexing can be paused, but it typically stems from a blocked queue or max disk space is reached. If searching is indeed functional, then you can try the following search to see what queue is blocked:
index=_internal source=*metrics.log* blocked
If your system is unable to search, then you likely have a corrupt index that needs repair. You should inspect your $SPLUNK_HOME/var/log/splunk/splunkd.log and look for FATAL or ERROR messages. Those messages should hint at what is causing the problem.