Okay, upon some more consideration, I can imagine only one interpretation of Marci that would lift the veil of contradiction without the need to resort to poor memory of Marci.
As Rene points out, Kircher did not knew Mnishowsky, but he knew Ferdinand III. So the whole point why Ferdinand III is mentioned at all is because he is invoked as a means to introduce Mnishowsky to Kircher and to arouse Kircher's interest. So Marci would write: "Dr. Rafael, once the language tutor of Ferdinand III, told me..." I suspect that Marci simply omitted the word "once", and it was precisely that what made his phrase a mess of a reference.
Insofar as Kircher knew Ferdinand III, Kircher really was not in need of additional explanations of who Ferdinand III was - was he a King of Bohemia, a Roman Emperor, or somebody else. So why Marci would even include the reference to the Kingdom of Bohemia? Even if Mnishowsky was still the language teacher of Ferdinand III when the latter was already King of Bohemia (but still could not force himself to master the Czech language, haha) - which is highly unlikely, as discussed above - why include these particulars into the letter to Kircher? Was it of importance to Kircher whether Mnishowsky had been the teacher of Ferdinand when the latter was King of Bohemia or rather at some other time? I don't think so. Hence, the whole note about Ferdinand's rule over Bohemia, and the Marci's "tum", must refer not to Mnishowsky's teaching Ferdinand, but to Mnishowsky making the Report to Marci!
In other words, what Marci says in quite a roundabout fashion, should be read in the following way:
"When Ferdinand III was King of Bohemia, Dr. Rafael, once his teacher in Czech language, told me that"...
As Rene points out, Kircher did not knew Mnishowsky, but he knew Ferdinand III. So the whole point why Ferdinand III is mentioned at all is because he is invoked as a means to introduce Mnishowsky to Kircher and to arouse Kircher's interest. So Marci would write: "Dr. Rafael, once the language tutor of Ferdinand III, told me..." I suspect that Marci simply omitted the word "once", and it was precisely that what made his phrase a mess of a reference.
Insofar as Kircher knew Ferdinand III, Kircher really was not in need of additional explanations of who Ferdinand III was - was he a King of Bohemia, a Roman Emperor, or somebody else. So why Marci would even include the reference to the Kingdom of Bohemia? Even if Mnishowsky was still the language teacher of Ferdinand III when the latter was already King of Bohemia (but still could not force himself to master the Czech language, haha) - which is highly unlikely, as discussed above - why include these particulars into the letter to Kircher? Was it of importance to Kircher whether Mnishowsky had been the teacher of Ferdinand when the latter was King of Bohemia or rather at some other time? I don't think so. Hence, the whole note about Ferdinand's rule over Bohemia, and the Marci's "tum", must refer not to Mnishowsky's teaching Ferdinand, but to Mnishowsky making the Report to Marci!
In other words, what Marci says in quite a roundabout fashion, should be read in the following way:
"When Ferdinand III was King of Bohemia, Dr. Rafael, once his teacher in Czech language, told me that"...