Correct me if I'm wrong, but I believe that as compared to a full or 6max table, Heads Up is a) much more psychological and read dependent and b) much more luck dependent. You may just be getting a visit from the variance fairy, but it is possible that there are leaks in your HU game. It is quite difficult to determine what they might be without taking a look at some stats or hand histories from your game.
However, in terms of general advice, I can share with you the tips that have greatly improved my HU game. All of this GREATLY depends on your opponent and his/her play, but in general the following tips still apply.
1) Aggressive, aggressive, aggressive! HU requires more aggression, especially PF, because it is so much more effective against a single player than it is against multiple, in the sense that its easier to scare one person off than it is to scare off eight. Use your aggression to bully your opponent, even if you are in the small stack. This means constantly raising from both SB AND BB if you have anywhere near a decent hands, firing c-bets on the flop and 2nd barrels on the turn. Pocket pairs are clear winners (especially with a small stack) as well as any two face cards. Connectors and suited cards go down in value. Don't be afraid to re-raise as well if you think he's just trying to re-steal.
Of course, if you run into a lot of resistance or the opponent also is UBER aggressive, you'll want to change it up and slow down by being more selective with your aggression until you sense some weakness in him. That brings me to tip no.2.
2) Adapt and change up your game to keep him/her guessing. If you've been playing super aggressive for several hands and have managed to steal some blinds, cool off for another couple hands until you get a good one, or just until you sense that he's getting "comfortable" again. If you're on your "cooled off period" and he starts to get aggressive and you land a monster, you can slowplay and take advantage of him thinking that now you're scared, etc. Basically, play mind games with him, and don't let him get inside your head.
3) Don't call AI without a strong hand. It's very tempting (especially when you're short stacked) to trust that Middle Pair weak kicker when he's pushing AI. It's better to save your chips until you are the one pushing him AI, even if you only have a marginal hand. Why? Because pushing AI is more effective than calling an AI simply because it gives you two ways to win: 1) you might have the best hand 2) he might fold. This has to do with paying attention and knowing when you are probably beat (how many hands can beat you in a given situation, what hand might he have?)
4) HAVE FUN!!! This is by far the most important tip I've ever received for poker in general, but for Heads Up in particular. Especially if it's a small tourney where the difference between 1st and 2nd place is a few dollars, why not just have a blast? Better for me to have a blast, and lose, than to be all stressed out and win, when I'm already assured 2nd place. And more importantly, when I'm doing it "for the fun of it" I find it's easier for me to be aggressive, and even easier to fold hands when I think I'm dominated. Maybe its just me, but having a "for the love of the game" attitude improves my game a lot, just because I used to really tighten up HU.
I'm no expert, but I hope you find this helpful. Best of luck,