Did you buy this system used? It sounds as if the the class of service that some extensions are assigned has toll restrictions enabled.
As I'm using the desktop software to program my system, I'm not entriely certain how to do this with the phone interface, but I think you will need to go into 601, enter the jack number of a phone that allows toll calls, and note the class of service that it has. For instance, if you can place toll calls from the phone on jack 1, go to feature 601 (the display will show 601 COS#), press NEXT (SP-PHONE on phones that do not have soft buttons), the display will show Jack NO?->, enter 01. The phone's display will show #01-1: COSx, where x = the class of service you want to give to other phones.
Next, select a jack where you cannot make toll calls from by using the SELECT button (on most phones, the AUTO ANSWER/MUTE button )and entering in the jack's number. Hit the NEXT button, and change the COS to 1 (or whatever the COS number was for the phone you previously checked). Hit the SAVE (AUTO DIAL) button to save the change and go on to the next extension. This isn't the best solution (that would be removing toll restrictions on all COS's), but I think this is the fastest and most accessable to someone not very familiar with the system.
I'm not sure why higher extensions would not give service to phones, but they might be configured as voice mail ports. How many and what ports are giving you this problem?
Hope this helps,
Sam