The "L" flag stands for "Last rule", meaning that if this rule was evaluated successfully then no subsequent rules will be evaluated. In URL rewrite module we have a rule attribute called "stopProcessing", which has the same semantics as L flag in mod_rewrite. The rule converter should set this flag to true when converting any mod_rewrite rules that use "L" flag. If that is not the case for you - could you post your rule here?
Also, the rule import tool understands only mod_rewrite syntax. ISAPI_Rewrite syntax, while similar to mod_rewrite, has some unique flags and attributes, so the tool will not be convert ISAPI_Rewrite rules reliably.