Why does my ThinkPad's battery stop charging at 98% or 99%?
Check if you have the latest BIOS update done for your ThinkPad via Lenovo Drivers page or via ThinkVantage System Update installed in your machine.
Check if there are any updates for your battery firmware via Lenovo Drivers page or via ThinkVantage System Update installed in your machine.
Do a battery gauge reset via following steps
Navigate to Power Manager --> Battery Tab --> Battery Maintenance --> Perform Reset. (screenshot below)
If all of the above have been done and the battery still seems to stop charging at 98% or 99%, this is because of the system has been designed to do a slow charge to improve battery life span. Do wait a while and the battery will be fully charged to 100%.