The plugin is trying to use wp_sph_counter, which does not exist (and is not created by the plugin). I suspect this is an old table that was removed in 3.1?
root@BlogTest2:/srv/blog.photobiz.com/sphinx# /usr/bin/indexer --rotate --all
Sphinx 0.9.8.1-release (r1533)
Copyright (c) 2001-2008, Andrew Aksyonoff
using config file '/etc/sphinxsearch/sphinx.conf'...
indexing index 'wp_main'...
ERROR: index 'wp_main': sql_query_pre[1]: Table 'photobiz_blog.wp_sph_counter' doesn't exist (DSN=mysql://pbblogweb:***@localhost:3306/photobiz_blog).
total 0 docs, 0 bytes
total 0.010 sec, 0.00 bytes/sec, 0.00 docs/sec
indexing index 'wp_delta'...
ERROR: index 'wp_delta': sql_query_range: : range-query failed: Table 'photobiz_blog.wp_sph_counter' doesn't exist (DSN=mysql://pbblogweb:***@localhost:3306/photobiz_blog).
total 0 docs, 0 bytes
total 0.010 sec, 0.00 bytes/sec, 0.00 docs/sec
distributed index 'wp_' can not be directly indexed; skipping.
Also, there is no option in the plugin to simply generate the config for a system-wide install. I have to do that manually by running 'php sphinx.conf' which seems a bit silly. I also don't like that Apache can read the Sphinx indexes - there should be an option to skip that (no need if using the system wide installation of Sphinx).