Have you checked in your startup objects if it installed something? Check in Activity Monitor if there's still an unknown task working. I have Activity Monitor always running, showing the CPU history in the Dock. The Activity Monitor is a very useful tool.

I don't know much about Time Machine, isn't it creating only a main backup folder in the drive you're using? I know the Time machine thing from another Mac forum who also wanted to hide this folder, and making it with invisible worked for him.

I'm invisibling (new word creation! ) files with Path Finder, it is a very powerful tool and a full Finder replacement. Of course it shows invisible files and is able to handle package contents (in apps, kexts, plugins etc) like normal folders. You also can correct file permissions very easily. The actual version is on the Demon. But because it's very powerful it's rather complicated to configure. If you want, you can have my settings.

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2 Opteron systems: OSx86 10.5.8, Andy's 9.8.0 kernel, Asus A8N-SLI Premium, Opteron 185 o'clocked @ 2 x 2,95 GHz (2nd system 2.6 GHz), ATI Radeon HD2600XT 256MB Dual-Monitor 2x HP L2035, 4 GB RAM, Griffin FireWave as main audio device, Marvell + nForce LAN, Asus U3S6 USB3/SATA6 card, 5,5 TB harddisk, Firewire 800 card, Apple Remote + eHome IR receiver, 2x Wacom serial graphics tablet, Canon Pixma iP4700, Logitech Internet Navigator wireless keyboard/mouse combination.

My Audio stuff: M-Audio Transit USB (default audio), M-Audio ProFire 610, M-Audio ProFire Lightbridge (34 channels) using Creamware A16 ADAT converter • MIDI: M-Audio Midiman 4x MIDI interface • Behringer Audio Mixers: Xenyx 1002, Xenyx 1002FX, Xenyx 1202FX, Eurorack UB1002FX, Eurorack MX1804FX, Eurorack MX262A • FX devices: Lexicon MPX100 DSP, Behringer DSP-1000 Virtualizer, Behringer MiniFEX 800 DSP, Behringer Multicom Pro MDX4400 compressor • RETRO: MSSIAH midi/sequencer/synthesizer cardridge for the C64 (Dual-SID), Steinberg M.S.I. MIDI Interface for C64