Indexes seems a most unlikely reason for this. I have some suspicions but I need more details...
1. Exact TimesTen version (output of ttVersion command).
2. All DSN attributes (from sys.odbc.ini file) for the database in question.
3. Output of 'ttAdmin -query DSN' for the DSN in question.
4. Please describe in fine detail how your INSERT program is working (down to the individual SQL statement and API call) and particularly when it connects to, and disconnects from the database.