You might have the currency and item cheats on for too long. See, every time you'd be spending gold/cheese/whatever, you instead gain that amount with these cheats. Given that your storage capacity is pretty low, you can easily end up with 100x or 1000x the amount of items you can actually store, but those don't just vanish, they drop as piles into the game world for your little guys to collect. With way too many items being lugged around you start getting slowdown, freezing and graphical bugs like characters leaving permanent after images when moving.
The solution is simple, turn off the cheats and either spend or sell the excess items.