There are two sets of rules for this Rule: two for C90 and two for C99. I am developing my program using C99 standard. Shall I unmark the two C90 rules and leave only C99 rules? (both 4 are marked by default)
The MISRA C configuration contains certain rules that are defined slightly differently for the C90 and C99 standard. These rules are explicitly marked in the headers as c90 and c99, so if the project is to be compliant with c99 then you only need to enable rules c99. For rule MISRAC2012-RULE_1_1, rules _b and _d check the limits for c99, and rules _a and _c for c90.