Sometimes shingles leak, but the foundation can leak too. If there is dry rot on your roof, water can get into your house. Check all possible entries, including looking for rotted wood, to make sure the problem is solved permanently.
If you need to walk on your roof, it is important that you do it at a time when it is not too cold or hot. Extreme weather tends to make shingles very brittle, so walking on them during this time can cause a lot of damage. Morning is the best time during summer months, and afternoon is best in the winter.