It seems that NVPS calculation logic of frontend is not syncing with server.

Here is the current svn code in frontends/php/include/func.inc.php:

// comments: !!! Don't forget sync code with C !!!
$row = DBfetch(DBselect(
'SELECT SUM(1.0/i.delay) AS qps'.
' FROM items i,hosts h'.
' WHERE i.status='.ITEM_STATUS_ACTIVE.
' AND i.hostid=h.hostid'.
' AND h.status='.HOST_STATUS_MONITORED.
' AND i.delay<>0'
));

In above code, it doesn't care the value of flags column in items table.
It means that items.flags = ZBX_FLAG_DISCOVERY_PROTOTYPE is included in calculation and distort NVPS value.

Trapper just ignores ZBX_FLAG_DISCOVERY_PROTOTYPE when checking active items in C code, so need to
do same thing in frontend, doesn't it?

I've attached a patch to fix this glitch between C and PHP code for svn HEAD.