First off you can charge an 11.1 volt lipo at 0.5amp or about 1/4C. It will take a long time to complete.
Stu,
You need to write out here how you are setting -up the charger so we can determine what you are or aren't doing correctly.
After you press enter and select Lipo Charge and press enter again the lower left number will flash (0.5a) and you press the right arrow to increase the amperage number. Press enter again and the lower right number starts flashing (11.1 v) pressing the right arrow changes the pack voltage (or number of cells) such as 11.1, 14.8, 18.5 , etc.... Then press and hold enter to verify pack and after confirmation press enter again to start the charge.

You need to solve your first disaster before moving onto the next ! However the transmitter packs you have are two different types. The 9.9v pack is a LiFe pack and requires you to make even more changes to your charger in order to properly charge it. Forget that until you can properly learn how to use the charger to charge LiPo packs. The second pack 11,1 volts is a LiPo transmitter pack and you can charge it as soon as you get the LiPo charger procedure down.
What you are referring to as 1 cell and 5 cell are the 1C and 5C ratings of the packs. 1C and 5C do not mean cells but rather Discharge Rate. Re-read that article again and scroll down to the section Discharge Rate.

Please list your step-by-step procedure for setting up your charger to charge an 11.1 volt /1800mah lipo at 1.8 amps using the LiPo Charge setting.