I hope you would be able to provide some advice as things are getting very frustrated. I am an EU national married to a Sri Lankan. At the moment I am in my home country and he is in Sri Lanka. We are planning to move to Czech Republic. Upon reading all the official websites of their ministries and such we came to the conclusion that we would get him a short-term tourist visa and once he is in Czech he would apply for a family permit. However, the Czech embassy has told me that they might not grant him a short-term visa if there is a suspicion he would stay in Europe? Is this Ok? Is our plan illegal? If so, what are you suggesting we do?
For the first 90 days of your stay in the Czech Republic, your husband should apply under the Visa procedures for the short stay of Family Members of EU Citizens (up to 90 days).
The visa application for family members of EU nationals is free of charge. The general processing time is fourteen days, but it might be extended, especially if the supporting documentation is not sufficient. In case of missing proof of the EU citizen identity and the family relationship, the applicant cannot be considered to be a family member of an EU citizen and standard rules of procedures will be applied.
He should be able to apply for his long-term residence permit after arriving on the short-term visa. As long as he is with you, he is covered by the EU right of freedom of movement, so he cannot be deported. If he stays in the country longer than 90 days without a permit, he could be liable for a fine, but no more.
Because you are able to stay together in the Czech Republic for up to 90 days with almost no conditions on your stay, this whole concern of whether the visa is a "settlement" visa is pointless. The relevant French version of these rules can be found at Européen en France : entrée et séjour de moins de 3 mois / Famille non européenne accompagnante. Perhaps if you point this out to the French Embassy they will have a better understanding of the kind of application you are making.
As you tell it, it seems completely off-base. You do in any case have a right to move to the Czech Republic (with a few caveats: you need to either work or have sufficient financial resources) and to have your spouse join you so it seems odd to refuse him a visa on that basis (and, indeed, the usual grounds for refusal like “your intention to leave the territory of the member states before the expiry of the visa could not be ascertained” do not apply to EU citizens' family). Are they offering another type of visa instead?
In practice, one thing you could do is contact the SOLVIT centre in your country of origin. They might be able to clarify your situation or even assist you by contacting the Czech authorities.