You wondered whether your daughter's status as an SLD student might hinder her chances of getting into college. An important issue here is whether your daughter's A-/B grades in the SLD classes are "equal" to the same grades earned by kids outside the SLD program. In some SLD classes, the curriculum is modified by essentially making it easier. If this is true for your daughter, she just might have difficulty getting into (and staying in) some colleges. In other programs for students with LD, modification means changing teaching strategies (so that they match the learning needs of the students) without compromising quality or lowering standards. If your daughter is working up to her capacity (that is her intellectual potential -- usually determined at least in part by IQ test scores), then her grades are probably a valid measure of her performance.
The fact that your daughter earned lower grades in the social studies class could be due to several things. It is possible that the course is not being modified as much as it needs to be (the teachers may not be teaching in the way she learns best). Also, if the regular education teacher does not have training or experience with students with LD, he or she may need more help from a special educator in order to teach your daughter in the appropriate manner. Another explanation is that your daughter is slowly but surely making the difficult adjustment from a self-contained special program to the environment of the regular class. The regular class might simply be more challenging than the SLD program. The fact that your daughter's grades have improved a bit is a good sign. I hope this trend continues.
You should be aware that having a learning disability should not impair your daughter's chances to get into a good college. Many colleges have excellent programs for students with learning disabilities. Descriptions in a college guide book will include this information, or your daughter's college counselor can help you.