A few ideas you might want to check :
- apart from Silk and Tinkertool settings, Safari has it's own font preference. Try changing it, perhaps there's a conflict.
- Silk has an Exclude list : try putting Safari in it.
- does Tinkertool do anything to Safari or any individual app, at all ?
- does your problem arises on some specific sites ? I've seen that happen (p.e. popup list to choose country), and visit these with Camino. So perhaps it's a Safari issue.
HTH