using version 6.2.2

What i did:
the other day i updated to 6.2.2 stoped started, removed all stones; replaced all stones and areas.
today i 'reload'ed the server to load another plugin.

Since i was eager to know if PStones was doin good i kept an eye on the log, i thought some "PreciousStones is saving and disabling' thing would appear but Precious Stones was not even heard of, follows reference Wall Of Text

2011-09-29 19:17:38 [INFO] �[35m[Server] Server will now reload, hold your horses!�[0m
2011-09-29 19:17:42 [INFO] xray detcetion disabled
2011-09-29 19:17:42 [INFO] Permissions saving data...
2011-09-29 19:17:42 [INFO] Permissions saved all data.
2011-09-29 19:17:42 [INFO] Permissions disabled successfully.
2011-09-29 19:17:42 [INFO] [AuthMe] Authme 2.0 disabled
2011-09-29 19:17:42 [INFO] [SimpleChestLock 0.11.1] Disabled!
2011-09-29 19:17:42 [INFO] [mChat] mChat version 1.7.12 is disabled!
2011-09-29 19:17:43 [INFO] Permissions was initialized.
2011-09-29 19:17:43 [INFO] [Permissions] version 3.1.6 loaded
2011-09-29 19:17:43 [INFO] xray detection enabled
2011-09-29 19:17:43 [INFO] Found and will use plugin Permissions v3.1.6
2011-09-29 19:17:43 [INFO] [Tips] Loaded 1 global tip set(s)
2011-09-29 19:17:43 [INFO] tipSetsForWorld: java.lang.ArrayStoreException
2011-09-29 19:17:43 [INFO] [Tips] Loaded 0 tip set(s) for world world
2011-09-29 19:17:43 [INFO] [Tips] Loaded 0 tip set(s) for world world_nether
2011-09-29 19:17:43 [INFO] [Tips] version 1.0.1 enabled
2011-09-29 19:17:43 [INFO] WeatherSigns v0.3 Enabled
2011-09-29 19:17:43 [INFO] [WeatherSigns] Permissions plugin found!
2011-09-29 19:17:43 [INFO] [AuthMe] Authme 2.0 enabled
2011-09-29 19:17:43 [INFO] [SimpleChestLock 0.11.1] Enabled!
2011-09-29 19:17:43 [INFO] Using locale pt_PT
2011-09-29 19:17:44 [INFO] Using locale pt_PT
2011-09-29 19:17:44 [INFO] Loaded Essentials build 2.5.7 by [Zenexer, ementalo, Aelux, Brettflan, KimKandor, snowleo, ceulemans, Xeology, KHobbits]
2011-09-29 19:17:44 [INFO] Loaded EssentialsSpawn build 2.5.7 by essentials team
2011-09-29 19:17:44 [INFO] Loaded EssentialsGeoIP build 2.5.7 by essentials team
2011-09-29 19:17:44 [INFO] This product includes GeoLite data created by MaxMind, available from http://www.maxmind.com/.
2011-09-29 19:17:44 [INFO] [mChat] A superperms Permissions plugin was not found, Checking for PermissionsEX.
2011-09-29 19:17:44 [INFO] [mChat] PermissionsEx was not found, Checking for Permissions.
2011-09-29 19:17:44 [INFO] [mChat] Permissions 3.1.6 found hooking in.
2011-09-29 19:17:44 [INFO] mChat is keeping usage stats an. To opt-out for whatever bizarre reason, check plugins/stats.
2011-09-29 19:17:44 [INFO] [mChat] mChat version 1.7.12 is enabled!
2011-09-29 19:17:44 [INFO] [SimpleClans] Version 1.6 loaded
2011-09-29 19:17:44 [INFO] [SimpleClans] SQLite Connection successful
2011-09-29 19:17:44 [INFO] [SimpleClans] Clans: 1
2011-09-29 19:17:44 [INFO] [SimpleClans] Clan players: 1
2011-09-29 19:17:44 [INFO] [SimpleClans] Payment method: Essentials v2.2
2011-09-29 19:17:44 [INFO] [PreciousStones] Version 6.2.2 loaded
2011-09-29 19:17:44 [INFO] [PreciousStones] SQLite Connection successful
2011-09-29 19:17:45 [INFO] PreciousStones fields: 5
2011-09-29 19:17:45 [INFO] [PreciousStones] Payment method: Essentials v2.2
2011-09-29 19:17:45 [INFO] Server permissions file permissions.yml is empty, ignoring it
2011-09-29 19:17:45 [INFO] �[32mReload complete.�[0m

On reload complete i then went and see if the areas were still intact. they weren't. which made me remove all the stones again, and replace them and the areas.
I got this while doing so:

2011-09-29 19:34:38 [SEVERE] Error at SQL INSERT Query: java.sql.SQLException: columns x, y, z, world are not unique
2011-09-29 19:34:42 [SEVERE] Error at SQL INSERT Query: java.sql.SQLException: columns x, y, z, world are not unique
2011-09-29 19:34:43 [SEVERE] Error at SQL INSERT Query: java.sql.SQLException: columns x, y, z, world are not unique
2011-09-29 19:34:44 [SEVERE] Error at SQL INSERT Query: java.sql.SQLException: columns x, y, z, world are not unique
2011-09-29 19:34:45 [SEVERE] Error at SQL INSERT Query: java.sql.SQLException: columns x, y, z, world are not unique

AND (and i kinda think this one isn't yours but) i have this one lying around (a bunch of'em actually), i cannot figure out what it is
2011-09-29 19:52:10 [INFO] Attempted to place a tile entity where there was no entity tile!

*note: some removed Precious Stones were mine (i was the owner) some i wasn't, there wasn't any difference in the 'behavior'; both types of Precious stones (those i was owner of and those that i wasn't) lost its area of effect.

That is normal. Its trying to save the pstone again to the database. Happens when you are using superpickaxe to break a pstone and then placing another in its place. Also in a couple other circumstances. you can safely ignore it.

What other circumstances should i avoid? because something wacky IS going on. Just now i've seen a2x2 area that's not within the city limits, but the adjacent blocks are protected by the city area.

maybe because i've been overlapping the same blocks its bumping into old data?

Also, there's nothing normal about pstones not working after a reload/start stop - but i'm not waving a mace, i'm just saying what's going on.

note: i have no superpickaxe of anykind. i dont even use worldguard or edit or whatever (tho im starting to think i should)

6.2 had a bug that was manifesting itself in many many ways. It messed up with the whole protection system. Try 6.3 and tell me if you still have the prob.