It is true that the General Instruction of the Roman Missal (GIRM, 2002) states that a person who kneels shouldn’t be denied Communion. It is also true that there are Latin-rite Masses at which it would be acceptable for communicants to kneel for Communion (e.g., Anglican-use Catholic liturgies, indult Tridentine liturgies). The GIRM, however, presumes that at a standard Roman-rite liturgy in the United States the communicants will ordinarily stand, and should be privately corrected if they do not:
The norm for reception of holy Communion in the dioceses of the United States is standing. Communicants should not be denied holy Communion because they kneel. Rather, such instances should be addressed pastorally, by providing the faithful with proper catechesis on the reasons for this norm (GIRM 160).
For a communicant at a standard Roman-rite liturgy to deliberately ignore the just instruction from a priest to receive Communion while standing, instruction given in accord with the liturgical rubrics approved by the Vatican for use in the United States, would be problematic indeed. We are called to be faithful to all just instruction given by the Church through its ordained ministers, not only to those instructions we like or understand.
As for your particular situation, I do not know enough about the circumstances to comment on the priest’s decision to give you permission to kneel. Perhaps you attend a liturgy at which kneeling is expected (such as the ones mentioned above). That said, it remains true that the normative posture for receiving Communion at standard Roman-rite liturgies in the United States is to stand. Those priests who, in accord with the GIRM’s instruction, do not refuse you Communion but give you private instruction to stand are no less orthodox on this issue than your own priest.
The Struggle for Uniformity in the Liturgy by Kenneth D. Whitehead