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You not there are most of the things about a target which are stored locally on the target rather than on the GC itself. For example, if you set t matrix value for a database target, it is stored on the database itself whether you use 10g or 11g GC . Here in your case, i think your both GC are fighting together to monitor a single target which is configured on both and i think it will not be supported (you can confirm from MOS). So my advise will be to configure your targets with only one GC (either 10g or 11g)
Running 2 agents on a server is not supported.