APC doesn't care about file extensions.  You must have 
something else going on with those files.  Any apc.filter 
lines in your config?

nope, I'm using php-fpm with ngnix all was working great until the update. So weird.

I have just these options

apc.shm_size="96M"
apc.rfc1867 = "0"
apc.num_files_hint="1128"
apc.user_entries_hint="512"
apc.mmap_file_mask=/tmp/apc.XXXXXX

I opened a discussion on 
http://groups.drupal.org/node/113594

It seems that the last correctly working version is APC-3.1.4

I also updated php to 5.2.16 with same results.

You need to look beyond the file extensions.  Like I said, 
there is nothing in APC that looks at the extension of a file.

I think i found something

.module files are loaded dynamically by Drupal:
by  drupal_load() who gets the the full path of the file from an SQL table. And then calls include_once

http://api.drupal.org/api/drupal/includes--bootstrap.inc/function/drupal_load/6

.inc files are loaded almost in the same way:
module_load_include() who gets the path from SQL and adds the filename and extension usually form static string declarations.

http://api.drupal.org/api/drupal/includes--module.inc/function/module_load_include/6

neither of the two "inclusions" seems to get cached onto apc.

Only include files included directly from static declarations from other files like require_once 'includefile.inc' or  are cached. .modules files are never loaded in this way. For that reason I can't find any .module files on the apc cache.

Does this make more sense?

Same issue. Just upgraded to 3.1.6, everything worked before 
the upgrade from 3.1.3.

I can confirm the behavior. Apparently apc doesnt want to 
cache dynamically included files:

This test:
<?php
$DYNAMIC_INCLUDE_ONCE = 'DYNAMIC_INCLUDE_ONCE.inc';
include_once 'INCLUDE_ONCE.inc';
include_once $DYNAMIC_INCLUDE_ONCE;

$DYNAMIC_REQUIRE_ONCE = 'DYNAMIC_REQUIRE_ONCE.inc';
require_once 'REQUIRE_ONCE.inc';
require_once $DYNAMIC_REQUIRE_ONCE;

?>

Results in only 3 of the four files being cached.
the 
include_once $DYNAMIC_INCLUDE_ONCE; 
Is failing to cache DYNAMIC_INCLUDE_ONCE.inc

apc.stat=0 rewrites all constant includes

so

include_once "foo.inc"

becomes 

include_once "/var/www/html/bar/foo.inc"

internally, while compilation happens. This does not happen
for dynamic includes. 

This issue with drupal < 7 has been reported and fixed 
already in svn (#20529).

Closing bug, please re-open if the svn trunk version fails.