Import records using phprunner import feature

I use import feature in phprunner 8.0 last build and 9.6 (27826) . In 8.0 I had a problem with import . The mapping feature would come up and the clicking the import data button would start inserting records. There were 5000 or so records. So I think it just timed out . So I split the excel xlsx file into 5 files and imported that way . It worked . Now I go into my output and try to enter data which some fields in different tables uses edit box as ajax lookup and I get the red square in all of my tables from that same table I imported records too nothing fills in from that table. If I restore database , it works fine again. Can't seem to figure this out. Does truncating records first in database mess up indexes or something I am stumped on this one. MYSQL
even tried bullzip excel/access and imported sql file in database and same thing edit as ajax fields would still not fill in.
In the past I used an event before insert without trucating table , but had issues here too.

$strSQLExists="select * from Customers where CustomerID=(" . $values["CustomerID"]. " AND EmployeeID=' " . $values["EmployeeID"] . " ')";

$rsExists = db_query($strSQLExists,$conn);

$data=db_fetch_array($rsExists);

if($data)

{
return false;
} else {
return true;
}

but it only just sat there processing records . It would process 1200 records and stop but the edit box as ajax popup would stil not work. custname field and custid dependent on customer.
update:

this also happens in 9.6 , I did not have output temp_c directory set correctly .