We have a single site collection where alerts have been down for some time. After review, it was suggested that client-side Javascript (common ones like EasyTabs and SPServices) could break alerts. I'm skeptical of that but wanted to see if it's even possible for client side changes to break alerts.
window
namespace. Never had a problem with SPServices, so you could probably out rule that file. I would start by removing all custom scrip references to see if that works, then add them back one by one till it breaks