Conflict issues are frequently found in commercial templates where there is a heavy reliance on scripting to provide fancy menus, slideshows, sliders and so on. It is not unkown for a template to load its own jQuery version (Artisteer templates very often do this so is a first place to check if you use that template system) and for an added slideshow module to load its own version. If you then have VirtueMart running on the page then that also will usually load its jQuery version.
Tools to detect conflicts can be Firebug's script debugger or Console error checker, or the debugger in IE9/10 developer tools.
Possible solutions could be uninstalling any module that causes conflict, a plugin such as Simple Image Gallery Pro or in some cases JoomSEF. Otherwise try using jQuery Easy or ReReplacer.
If your template uses bootstrap.js then to solve a script error with VirtueMart's jQuery (version 1.6.4) you can replace that VM version with jQuery 1.7.1 - in com_virtuemart/assets/js/ the script is named jquery.min.js VirtueMart 2.0.x and fancybox will still work with that version.
There should be less conflict issues with VM3.x. From the VM3 release news "The new jQuery versions are now mainly the same as in Joomla 3.3 (jQuery v1.11.0,jQuery UI - v1.9.2, legacy complete). Shops using Joomla 2.5 with VirtueMart 3 also benefit from this. It prevents needless configuration problems."
jQuery Easy (rarely needed with J3.x VM3.x):http://extensions.joomla.org/extensions/core-enhancements/performance/jquery-scripts/18327