Report issues in this thread. Please always provide complete debug log. See Log_file (wiki) on the wiki for how to. If you do, it will be looked and I will try to help.
If this happens you most likely have an application running that continuously reads and/or deletes files in the media source. Remove the offending application or remove the folder from media sources in xbmc. Normally, downloading applications and such should not cause this as all file modifications and creation/deletion of non-media files are ignored.
"Failed to watch x" on Linux
On linux there is a limit on how many folders you can watch simultaneous. If your media sources contains more subfolders than the limit (usually 8192) it will fail. Select "Polling" under "Method" in add-on settings, or increase the inotify watches limit.
Issue in xbmc http://trac.xbmc.org/ticket/14212 Only known to affect Polling
If using polling, will it hog the disks and prevent them from spinning down
No. When there's nothing being written to the drives, the OS will usually cache the entire directory structure. If for some reason disk activity persist, you might want to look into increasing the cache space in you OS.
If you are experiencing performance issues you can select another method for network shares. Here's an explanation of the different polling methods you can choose:
Depth inf. (default): performance dependent on total number of directories and files. Will detect everything, also whether a file was added or removed.
Depth 1: cpu/network cost ~0. independent of number of files
folder a/ <-- detected (will always scan and clean (if enabled). unknown if it was added or removed)
folder b/ <-- not detected
Depth 2: performance depends on number of directories and files in top folder (media source) only
folder a/ <-- detected as new
folder b/ <-- detected (will always scan and clean (if enabled). unknown if it was added or removed)
folder c/ <-- not detected