Some people have had issues with crosstalk from the HDMI cable into the aerial lead, causing loss of Freeview channels. Generally you can prove this by setting the HDMI output to one of the lower resolutions such as 576. If this makes the reception better, try another HDMI lead and also try to keep the HDMI cable and aerial leads as far apart as possible and at right-angles to each other if you can.
iNspectorgadJet might have a good point too - there are two sets of aerial connectors on the back panel - one for the digital tuner and one for the analogue. If you want to use both, you need to put the aerial into the input of one and a loop cable from the output socket into the other input, then from that output to the TV.