Problem with equation labels

I have a document that has equations with labels: 

\begin{equation}
\label{eq:1}
y=x
\end{equation}

In the past the Latex compiler would find the labels and then allow me to reference them, as in \ref{eq:1} or sometimes \eqref{eq:1}. However, on the latest version, which I updated yesterday Jan 5 2012, the compiler cannot find the labels and gives Eq.(??) in the text and an error message: LaTeX Warning: Reference `eq:1' on page 1 undefined on input line 62. This is independent of how many times I run the code (usually it has to run twice, first to list the labels and then again to reference them.) The document compiles ok on a Mac using a different compiler but not on this version 9 of MiKTex under Windows 7 (32 bit). Figure labels work fine. Is this a bug?

Regards

Tim 

------------------------------------------------------------------------------
Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
infrastructure or vast IT resources to deliver seamless, secure access to
virtual desktops. With this all-in-one solution, easily deploy virtual 
desktops for less than the cost of PCs and save 60% on VDI infrastructure 
costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox