Google updated it’s Custom Search Engine (CSE) to v2 as of last weekend. As a webmaster, this is good news all-around. The new version features an improved control panel that automatically makes changes to the search user-interface without requiring updates to your site-specific code. Previously, all page elements would load simultaneously which caused a brief drop in site performance. To fix this Google has changed search page element loading to be asynchronous, or to load individually. Client-side widgets can now also be customized using the HTML syntax found on this page.
CSE v1 will remain supported for some time, but if you use this Google service for your website you should head over and update sooner rather than later.
via [Google Custom Search]
Seems like the GCS v2 is leaving some developers hanging, in regards to IE9: http://productforums.google.com/forum/#!topic/customsearch/ZIwVtE2i73E%5B1-25%5D