Since your GC application is in process, there might be complications. Check with your lawyer before you step out of the country, as doing so might jeopardize your GC application. BTW, the fact that you got your H1B shows that your skipping first semester is not an issue anymore. Your grades should not be any concern to those immigration people. Heck, you got a job at Fortune 100 company, right? If the employer in such excellent standing thinks you are good enough to be their employee, then why on earth should an immigration (govt) clerk with probably no or dismal college record judge you.