Thanks for the replies and the help all. :)
Will check for latency on the ports and check back.
The computer itself isn't too old. The CPU in there is a AMD FX 8350, an eight core at 4hz. 16 gigabytes of RAM. The DAW itself is FL Studio 11. All running on Windows 10. I do have some stuff running alongside my DAW, but nothing demanding. Google Chrome and the like. Shouldn't really be anything the CPU can't handle. Thing is, CPU handles it fine as long as it's running through the 'internal' soundcard, the trouble starts when using the soundcard in the Helix (or PodXT for that matter).
Also, just want to point out this doesn't sound like the latency issue of loading too many plugins or something. Then it's 'stuttery', kind of jittery. But this is reeeaaally chopped, like a chop of sound of a half a second to a second, interspersed by a few seconds of nothing.
It doesn't just do it with FL Studio either. It'll do the same thing when running other audio (soundfiles, YouTube etc.) through the external soundcard.
EDIT:
Checking back already. Ran DPC Latency Checker and it showed extreme latency in the system. I tried disabling/enabling a few devices and one of the usb-ports was disabled. When I enabled it, latency dropped dramatically. Now, it doesn't seem to matter if it's on or off. It stays medium latency, spiking into high at times. Can't really find another device that affects latency.