Most of the aligners does not care about lower and upper case unless there is an option in an aligner and you told the aligner to skip lower case. Is there any specific reason that you specially made intronic region lower case? One reason what I see can be that you do not want your reads to map at intronic regions. For that I will suggest to replace those regions with N's. Or if you have some other reason and you want to keep them in lower case and also want that your reads should map at those positions, then just tell your aligner (or run in default, whatever aligner manual says) to not to differentiate between lower and upper case.

Also I would suggest that when ever you have some problem like this, you can always create a very small test fastq file (or fasta file of reads) and small genome file (fasta file) and then run your favourite aligner on these files. It will hardly take 5 minutes to run but good thing is you can play around with different options and you will learn lot of new things (I did the same thing and believe me every time I learn something new).

The meaning of lower and upper case can be different, repetitive regions etc.

In general aligners treat the upper and lower case bases identically unless clearly stated otherwise.

lower-case reference sequences can mean "mask" (i.e. don't align to this region) to some older aligners like BLAT, but not many short-read aligners care about this. See: http://www.biostars.org/post/show/3232/which-aligners-recognize-soft-masked-repeats-in-reference-sequences/