Hi EmpowersBane,
I'm with Consumer Products guy. What you're doing with the small C18 "trap" column is fairly commonplace, at least in places where I've worked previously. The only effect I'm aware of in using kinked tubing (after the analytical colum and before the detector) is that the laminar flow profile of the peaks can be improved a bit, Peaks Can be Narrower, less bandspread.
With the UHPLCs, the only thing I can think of from my own experience, especially with these "extra" connections, is the possibility of tiny microleaks--if present, these may cause baseline artifacts such as those you're experiencing. Sometimes these are hard to ID from the pressure trace and you have to hold Kimwipe at each connection to ID a microleak source.
Something to try...Best Wishes! Kinked tubing should not be a problem--unless the connections aren't quite up to snuff.