hmm seems as though you hadn't set up the schematics properly with regards to supply nets and/or you hadn't updated your pcb. If you did there would be supply net rules under the signal integrity section of the DRC dialogue in the pcb editor. Thats probably why you were getting 5V signals when you ran signal integrity as I think thats the default if you dont set supply nets properly.
Here's what I would do with your project. Go through and remove all the PCB layout directives that contain signal integrity rules from your schematics. Go through each schematic, check the document parameters and delete all rules from each of them... Its alright to leave the default "undefined rule". Save all the schematics, compile the project and update your PCB (make sure its part of the project) When you now go to your PCB document and check the design rules you should have no rules in the signal integrity section.
Go back to the schematic where you power ports originate, presumably the power supply sheet and place pcb layout directives on the each of your power nets as follows
- Place->Directives->PCB Layout
- Before placing the layout symbol, press TAB
- Click the edit button to edit the existing rule or add as a rule if nothing is there.
- Click on Edit Rule values, scroll down to the bottom and select Supply Nets under the Signal Integrity section
- Enter the appropriate voltage, Click ok on each dialogue to close them
- Place the dorective on the power net
- Do this for each power net
- Dont forget to place one attached to a ground port with the voltage set to 0
Recompile your project, keep an eye out for any error or warning messages from the compile then update your PCB. You should now see Supply net rules in the DRC dialogue
Now run the signal integrity, making sure to check that all model assignments are correct before doing so.
If you still get 5V signals where you expect 1.8V then you may have to check the IBIS files by finding out what model the driver pin has assigned, finding its definition in the IBIS file and seeing what the typical, min and max values are for the keyword [Voltage Range]
Hope this helps