I believe Auto-manage slots is not working as intended.  Mt settings are below.

Running 64-Bit Linux Build v2.59
Incoming bandwidth limited to 15700 KBps and turned on (button is pressed so text box is editable)
Settings->Transfers->General
Download slots set to 220 (hard set while trouble shooting.)
Auto-manage slots. Downloads is ticked.
If I click details:

<downloadautoskipqueue
maxextraslots=1000    //max extra download slots, can be a plain integer, was set a long time ago so there shouldn't be a cap that I run into
windowdur=170    //look at bandwidth going back this many seconds
windowtaperdur=10    //and this many additional seconds with a weight tapering to zero
avgdur=25    //average speed must be maintained over this many seconds
minratefactor=700    //no action until it's been this many seconds since a download started running (not queued)
stopwait=45      //no action until it's been this many seconds since a running download was re-queued or stopped
startupwait=180    //no action until it's been this many seconds since program startup or offline state (no dht traffic for 20 sec)
/>

I noticed my incoming was only at around 1500KBps with no new downloads being initiated over a 5 minute window.  I have 500+ in the queue.  I restarted client (standard troubleshooting) and issue has resolved.   Will monitor and see if I can reproduce.

Just adding possibly relevant information.  One of the disks that some, but not all, of the transfers were being saved to was full.  Possible it may have had an impact but IMO it shouldn't have.  The other transfers were on a disk that was not full.