mod_usertrack improperly makes a call to apr_table_setn to create the "Set-Cookie" header. If another module has run before mod_usertrack and added it's own "Set-Cookie" or "Set-Cookie2" header, the data is lost. This affects both Apache 2.0 and Apache 1.3. A call to apr_table_addn instead may be more appropriate (mod_usertrack.c, line 191).
Fixed in 2.1 and proposed for backport into 2.0 and 1.3 branches. Thanks for the report and thanks for using Apache.
*** Bug 26693 has been marked as a duplicate of this bug. ***