Sounds like they have air in them, when you pump them they air goes to the top of the reservior, much like many other brakes. Guessing you air got in when you let fluid out?
Given they’re a closed system (you have to adjust for pad wear, theyre fairly easy to overheat) youll want them to bled up properly, wheres most auto adjust open systems youll mostly get away with them having air in them in the UK, and just avoid turnign the bike upside down
I couldnt find my giant bleed kit last time I wanted to bleed them (was suppsed to come with the bike, was supplied when enquired about how to bleed).
Turns out the avid bleed kit (IIRC the formula one might also work?) has the same reservior fitting, then you just want a pipe (ideally clear) to fit onto the caliper bleed screw and into your waste fluid container
EDIT: your pics are showing to me now, your lever looks identical to my MPH3s (off a 2006 XTC), but your caliper completely different (mine are IS mount not post mount)
I know they updated them to MPH root, but I thought they were supposed to be an open system so they wouldn’t be able to use the older levers with the adjuster wheel?
Also it doesnt look like the pads of the caliper line up with the rotor? Is the rotor a giant one or not?
I know my brakes used a giant 164mm (not 160mm) rotor, though the braking surface was really wide such that a 160mm rotor would ‘work’ but not with rotor to spare on the inside like yours do?