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.Comment: 29 pages, 12 figures, accepted for publication in Ap