Even if you were baptized in another church that baptism wouldn't matter because a baptism must be performed with the proper authority and priesthood, which has only been restored to The Church of Jesus Christ of Latter-day Saints.
I would recommend visiting with your bishop/branch president to share your feelings and concerns with him regarding coming back to church. If there is anything important you need to share with your authorized priesthood leader, or anything you need to repent of, he will openly listen to you and help you return to full activity in the Church.
It's never a problem to come back to church because the Lord's arms are always open- ALWAYS! In this imperfect world there are people who aren't understanding or who may say/do things that are hurtful, but remember that they are human and that only God and His Son, Jesus Christ are perfect and they love you perfectly.
I would highly suggest praying for the courage and strength to start coming back to church, especially as Satan will try to stop you from doing what you feel and know is right. Move forward with faith, God will be with you.