When recording, Audio Hijack Pro's recording status line (found under the Record button) may indicate that skipping has occurred, as seen in this image:
Use The Root Hard Drive
We've seen problems with skips when people record to an external firewire drive. From a technical standpoint, this should be no problem, as firewire is plenty fast. Nevertheless, switching the destination to the root hard drive (the one on which your System is installed) may clear up skipping.
Save CPU
The other thing you can do is reduce the amount of CPU Audio Hijack Pro needs, and increase the amount of available CPU. More details are outlined below.
1) Quit processor-intensive applications: OS X allows many applications to run at once. However, some applications take up a lot of CPU, such as iTunes. If you don't have to have these applications open for the recording, quitting them may help.
2) Switch To Custom MP3: In the Recording Format menu, choose the Custom... Set this to MP3, CBR, Stereo, the desired bitrate. Then, turn the Quality slider down.
3) Switch to a lower bitrate MP3: The lower the bitrate set for encoding, the less CPU will be used.
4) Switch to another format: AAC encodes faster than many MP3 types, so this may result in fewer skips. Even faster is ALAC, and finally AIFF. AIFF is the absolute fastest way to record, using the least CPU, and you can easily post-process it to MP3, AAC, or ALAC right from the Recording Bin.
5) Turn off Effects: Effects in the Patch area use CPU to do their processing. Turning these off (by highlighting and pressing the Delete key, or by choosing None from their Title menus) will conserve some processor power.
6) Turn off Level Meters: Level Meters use a small amount of CPU power. Turn off the Levels in the Effects tab by clicking the bar that indicates their type ("In Peak", for example). The level meters in the control area can also be turned off, by Control-clicking and choosing Off.
If all else fails...
If these steps haven't fixed your problem, please (please!) email us for support and include information on your system. Send mail to audiohijackpro@rogueamoeba.com, and we'll try to get your issue solved.