When using Blockdata command to edit the contents/item in a flowerpot the pot requires a blockupdate to view the change.

To recreate, simple place a Flower Pot and enter:
/blockdata ~ ~ ~

Data value must be specified, any value will work from 0-8.

The pot visibly remains empty but when running:
/blockdata ~ ~ ~ {}
Tells you that the data specified above is present.
A blockupdate is required to view the contents, simply place a block around any of the pot's sides to make the update occur.