"Does one rule out the other?" the jester said, quickly ducking into cover.
Most probably the accursed bins, as the long standing bin access locking issue causes their contents to be unavailable (and thus invisible) when someone locks a bin for access (which happens well in advance of the actual access).
I'd try to designate what can be designated to be sent to the trade depot. Once dorfs drop what they're doing and start to haul stuff to the depot the bins ought to get free, giving you a second pass at designating them.
Seeds: Seeds are stored in bags, and those bags are subject to the same access issues as bins are, so when a dorf hauls a seed to a bag the planter can't find the seeds in that bag. You didn't specify which kind of access problem you had, though, i.e. the farm plot saying there are no seeds (which I think looks at the stockpile, not what's accessible at that particular moment), or if it's the planter issuing reports that there are no seeds. The latter issue usually resolves itself without overseer intervention.
@doublestrafe: Mountains do not support anything but grass, and even that might not regrow. Farm plots in different biomes support different crops, as noted, and you need 6 biomes to cover every booze producing plant (and unless you manipulate things, you're very unlikely to get them all, and bananas are bugged so you won't get those without modifying the raws [I've made them yield wood when cut, which does cause them to appear when eligible]). Finding biome boundaries isn't that easy, so I use a script to visualize the biomes.