First of all, _setCustomVar must come before _trackPageview.
Now to your problem:
This happens because User level custom vars are stored in the cookie. Since both your trackers share the same cookie the second tracker will be sent with the vars set on the first tracker.
You have 3 options.
1) Go With Universal Analytics
The right path here is to use Universal Analytics. Multi-tracking is not officially supported in Classic because it's buggy, as you probably noticed. And things are easy to break.
On Universal all custom dimensions are evaluated server side so this setup is supported. No data is stored on cookies for Custom Dimensions.
eg:
Provided you configured dimension1 on UA-XXXXXXX-1 and dimension2 on UA-XXXXXXX-2 through the Admin interface.
ga('create', 'UA-XXXXXXX-1', 'auto');
ga('send', 'pageview', {
'dimension1': 'cv1'
});
ga('create', 'UA-XXXXXXX-2', 'auto', {'name': 'newTracker'});
ga('newTracker.send', 'pageview', {
'dimension2': 'cv2'
});
More info:
2) Keep Classic Analytics but, use session level customVars
If you definitively can't move to Universal Analytics and want to keep using Classic you can get around this issue by just using Session Level Custom Vars. To make it work you would only need to change the scope of the custom Var as seen below (from 1 to 2).
Unlike User scoped Custom Vars, Session Scoped CVs don't get stored on the cookie. So you will get around this issue. The downside is that the value will only be valid for that session, not future sessions from the same user.
_gaq.push(['_setAccount', 'UA-XXXXXXX-1']);
_gaq.push(['_setCustomVar', 1, 'customVar1', 'cv1', 2]);
_gaq.push(['_trackPageview']);
_gaq.push(['second._setAccount', 'UA-XXXXXXX-2']);
_gaq.push(['second._setCustomVar', 2, 'customVar2', 'cv2', 2]);
_gaq.push(['second._trackPageview']);
3) Keep Classic and User scoped CVs but use different cookies per tracker
You can configure GA to create 2 sets of cookies, one for each tracker one at the root domain and one at the subdomain.
If your site is: http://www.example.net setup your trackers like this:
_gaq.push(['_setAccount', 'UA-XXXXXXX-1']);
_gaq.push(['_setDomainName', 'example.net']);
_gaq.push(['_setCustomVar', 1, 'customVar1', 'cv1', 1]);
_gaq.push(['_trackPageview']);
_gaq.push(['second._setAccount', 'UA-XXXXXXX-2']);
_gaq.push(['second._setDomainName', 'www.example.net']);
_gaq.push(['second._setCustomVar', 2, 'customVar2', 'cv2', 1]);
_gaq.push(['second._trackPageview']);
This MUST to be done in all pages of your site. Not only this one. This will make sure that each tracker uses it's isolated cookieset and customVars won't leak from one to another.
Notice that if your site can be accessed without www.. eg: http://example.net/ this will fail and there is no workaround. You can't create 2 sets of cookies with the same name in the same domain and path. You just can't.
Also if you use _gaq.push(['_setDomainName', 'none']); or _gaq.push(['_setAllowHash', false]);, the above trick won't work and cookies will conflict. Your data will be weird. Just don't do it. You've been warned.
I can't stress enough that this is provided without guarantees and if your data breaks it's on you. Multiple trackers are tricky and that's why it was never officially supported.
More info:
