It's definitely not the same problem. Clathrates are methane, for one thing, and the permafrost issue will cause CO2 emissions. Clathrates are in the water, permafrost is soil.

They are both associated with historically cold environments that are now warming up, but each has its own mechanism and likely impacts (clathrates may be worse, since methane is a much more powerful greenhouse gas, but the permafrost melting is going to be with us for 1000's of years whereas methane will be with us for "only" a decade. Also permafrost is likely to be a potent methane producer as well while it thaws out.

They are both examples of positive feedback loops that result in abrupt changes to the climate, yes. But, because they are different systems, the feedback loops behave differently. Methane trapped in sea ice is studied and modeled separately from organisms frozen in arctic permafrost.