Seghol + geminate occurs in conjugated forms and forms with enclitics, e.g., ʾettənénnâ "I will give it" (Gen. 13:17). In stems original /i/ is the source of seghol, and stressed /i/ in closed syllables (including syllables closed by geminates) became /a/ (baṯ < *bint-) or open (ṣéḏeq < *ṣidq-), and unstressed /i/ in closed syllables remained unchanged (tišʿâ). Grammatical morphemes and clitics show some additional processes, so you still get forms like first person ʾe- in closed syllables in conjugated forms, like the above, and then you also get loans like Nebuchadnezzar (-eṣṣar).
If there are any exceptions in the native stems, I don't know them. They should all follow the above rules for closed syllables.