So it seems I may have found the problem I'm having with my VHF / UHF setup. I took some readings on HF frequencies and everything seems fine. After a little research, I discovered that a PL259 plug is apparently at it's limits at 100 MHz. A better choice for these bands would be the BNC or N type connectors. A quick reference to Wikipedia states:
Despite the name, the (PL259) UHF connector is rarely used in commercial applications for today's UHF frequencies, as the non-constant surge impedance creates measurable electrical signal reflections above 100 MHz.
Either this had slipped my mind or I never new about it! I have never liked the PL259 plug, but most radio equipment is manufactured to take these plugs. So it looks like I'll be doing some conversions. Caution is required because not all BNC plugs are the same. Some are only for CCTV applications and are probably not suitable. They need to be stated as 50 Ohms and for up to 3GHz usage. Also, if using the screw-in type, it is a good idea to check for continuity and short circuits on your coax afterwards. (I speak from experience here!) There are some handy converters on the market - see below.
Update: