ERJ175 Captain reports missing an assigned crossing restriction of 12;000 FT on the CLIPR 1 RNAV to DCA after the FMS has been programmed to comply with clearance. The flight is then cleared direct to BAL and programmed by the Captain. A few moments later the aircraft is found to be proceeding direct to EYESS and the crew is again questioned by ATC.

Narrative

Flight at FL220 ATC assigned us to cross CLIPR at FL120. MCDU was programmed by non flying pilot and verified by pilot flying. It was also observed to be correct by the non flying pilot on the vertical profile. Aircraft was stable on VNAV descent; when we were questioned by ATC about our crossing restriction issued. When we both looked at our flight status; we were over CLIPR at FL132. Approximately 1;200 FT MSL off altitude. We were issued a heading for vectors to continue to FL100 due to this deviation. After the heading we were re-cleared direct to BAL. The pilot flying set the MCDU and the non flying pilot confirmed. The aircraft was put into LNAV mode and began heading in the proper direction. A few moments later we noticed we were off course again. The MCDU had dropped out BAL and replaced it with direct EYESS. ATC then questioned our navigation once again. We notified them we were having some navigational issues and corrected course again. The aircraft was placed in LNAV mode to re-intercept the course from PPOS [present position]. After the FMA indicated capture of LNAV; the aircraft was still under command of the heading bug for a few moments. After this; navigation was normal again and the flight was completed with no further issues or incidents.