Permissions.yml:
http://pastebin.com/Mae0DsiB

PreciousStones config.yml:
http://pastebin.com/Rve95x44

Server.Log:
http://pastebin.com/8LTidUH0

False Limits Bug:
If a player places a protection block (force-field block), disables it, and destroys it himself, it acts like it was never destroyed to the limits (confirmed in /ps counts) if the breakable-on-disabled flag is set to true. It is NOT an orphaned block, i used /ps clear to confirm. In line 97 of the server.log it shows Player destroying Players Iron Protection, when it should be Player destroyed HIS Iron Protection, as shown in line 106.

False limit break:
2012-02-10 22:11:09 [INFO] [PreciousStones] Player destroyed Players breakable Iron Protection field [IRON_BLOCK|-240 70 -71]

Regular Break:
2012-02-10 22:14:30 [INFO] [PreciousStones] Player destroyed his Iron Protection field [IRON_BLOCK|-240 70 -71]

allow-only-inside/allow-only-outside not working:
Also, can not seem to get either allow-only-inside or allow-only-outside flags to work, i pasted my permissions.yml and (preciousstones) config.yml in pasetbin. Server.log shows full start-up so you can see which plug-ins were running at the time (although i also ran it with just permissionsEx and precious stones and it still didnt work so i dont think its a conflict.) I am really depending on being able to fix the allow-only-inside/outside flags to work, so i hope you can fix it soon, or find where i went wrong! ^^

Best of luck,
Mathis

Checking this out.

You have the same spacing errors in the allow-only-inside lists, line 604 in here for example http://pastebin.com/Rve95x44, you are making the same mistake in all places you are using allow-only-inside.

Lines 67, 129, 148, 196, 211, 229, 277, 292, 311, 359, 376, 394, 442, 458, 476, 524, 540, 604, 620, 666, 674, 719 all look to have the same spacing error.

This is weird, I copied it straight from my config.yml, but in my config there is none of these spacing errors. Must have copied into paste bin wrong. The raw data shows it with correct spacing, but the main code shows only one space on those lines. Please assume I have all spacing correct, and look at it again. I just took my config.yml into a parser and it looks fine there. Ill look into why paste bin decided not to paste in correctly, it should not have done that since i used the yaml code for the paste... >.<

Your problem with the allowed-only-inside and allowed-only-outside flags is that you are writing the flag wrong, its "allowed" not "allow"

Wow, i feel stupid. LOL thanks for the help, i appreciate it!