Zabbix 2.2.0
MySQL 5.6.14
Ubuntu12.04

We had a similar problem on our proxies using MySQL :

20127:20140218:104924.341 Received configuration data from server. Datalen 14475347
20127:20140218:104926.241 [Z3005] query failed: [1062] Duplicate entry '11694-net.if.in[isatap.BT0D0000.w2k.bouyguestelecom.fr]' for key 'items_1' [update items set status=0 where itemid=261523;
20127:20140218:104926.486 [Z3005] query failed: [1062] Duplicate entry '13139-net.if.in[isatap.BT0D0000.w2k.bouyguestelecom.fr]' for key 'items_1' [update items set status=3 where itemid=416551;
20127:20140218:104926.508 [Z3005] query failed: [1062] Duplicate entry '11887-custom.process[CTIADM,cpu]' for key 'items_1' [insert into items (itemid,type,snmp_community,snmp_oid,hostid,key_,delay,status,value_type,trapper_hosts,snmpv3_securityname,snmpv3_securitylevel,snmpv3_authpassphrase,snmpv3_privpassphrase,formula,logtimefmt,delay_flex,params,ipmi_sensor,data_type,authtype,username,password,publickey,privatekey,flags,filter,interfaceid,port) values (1221282,7,'','',11887,'custom.process[CTIADM,cpu]',300,3,0,'','',0,'','','1','','','','',0,0,'','','','',4,'',null,'');
20127:20140218:104926.680 failed to update local proxy configuration copy: database error

queries failed -> database error, but proxies don't stop working
It seems its always the same few items that appear to cause duplicate entries.

Your database is not configured as case-sensitive. You need use utf8_bin collate instead of *_ci.

To solve the issue you need to execute it for each table:
ALTER TABLE <table_name> CONVERT TO CHARACTER SET utf8 COLLATE utf8_bin

I close the issue as Won't Fix.