Hi Jim,
The variance - covariance matrix is sometimes missing from the output for some models on both versions (I've ran them on 2 different machines (vista and 7), with either PRESENCE version 4.3 and 4.6). Interestingly, using a different species with the same data set the v-c appears in the output. Also note that in v. 4.6 I was able to view the c-v matrix by re-running models and selecting "print v-c matrix". While ultimately I was able to find the v-c matrix, I thought I'd pass this along as I suspect this is a bug...