We present evidence that the integrated profiles of some millisecond pulsars exhibit severe changes that are inconsistent with the moding phenomenon as known from slowly rotating pulsars . We study these profile instabilities in particular for PSR J1022+1001 and show that they occur smoothly , exhibiting longer time constants than those associated with moding . In addition , the profile changes of this pulsar seem to be associated with a relatively narrow-band variation of the pulse shape . Only parts of the integrated profile participate in this process which suggests that the origin of this phenomenon is intrinsic to the pulsar magnetosphere and unrelated to the interstellar medium . A polarization study rules out profile changes due to geometrical effects produced by any sort of precession . However , changes are observed in the circularly polarized radiation component . In total we identify four recycled pulsars which also exhibit instabilities in the total power or polarization profiles due to an unknown phenomenon ( PSRs J1022+1001 , J1730 - 2304 , B1821 - 24 , J2145 - 0750 ) . The consequences for high precision pulsar timing are discussed in view of the standard assumption that the integrated profiles of millisecond pulsars are stable . As a result we present a new method to determine pulse times-of-arrival that involves an adjustment of relative component amplitudes of the template profile . Applying this method to PSR J1022+1001 , we obtain an improved timing solution with a proper motion measurement of -17 \pm 2 mas/yr in ecliptic longitude . Assuming a distance to the pulsar as inferred from the dispersion measure this corresponds to an one-dimensional space velocity of 50 km s ^ { -1 } .