The jerky action of the chain, or "Chain Surge" is normally attributed two things. Lack of proper lubrication, and poor design.
As mentioned above, the chain will experience a slight variation of speed due to the action of the roller meeting with the working face of the tooth. During this meeting, the chain is being put through "chordal action". The extent of the chordal action is relative to the number of teeth in the driver sprocket. The more teeth, the less vertical chordal action the chain encounters.
It is possible that the elevated guides are taking the chordal action of the chain into account, and if designed properly, would be correct to do.
Many time a drive that experiences lots of motion due to chordal action can relive some of the surge by replacing the driver with a larger diameter sprocket.
In my experiences, the main contributing factor to chain surge of roller chain conveyors, or for any type of endless conveyor for that matter, is lack of proper lubrication.
Roller chains demand lubrication. A roller chain conveyor should have automatic lubrication equipment mounted. Periodic manual lubrication normally does not provide the lubrication frequency that the chains require.
Even when the chains are being lubricated, often times the drive chain is neglected, and can be a major source of chain surge once it has elongated past rec. limits (>2-3% of original pitch)
And with that said, it is also possible, as mentioned above, that your chains have elongated more than 3% past original pitch length. This causes the chains to have a mismatch of pitch with the sprockets. If you measure a ten foot section of the chain and compare the original pitch length with that of what it is today, you will know the percentage of elongation the chain has experienced.
If your chain is indeed longer than 3% of original length, both the conveyor chain and the sprockets need to changed out.
One more point I might add...if there is a tensioning take-up unit on the chains, it is possible that it has reached it's workable limit and needs to be adjusted. Or, it may be mechanically damaged or blocked from working correctly. Sometimes addressing this is all that is needed to smooth the run of a chain out.