I have very similar issue with my custom defined keyboard layout. Here it is

;;========================================================

(quail-define-package

"russian-no-windows" "Russian" "RU" nil

"ЙЦУКЕН Russian computer layout"

nil t t t t nil nil nil nil nil t)

;; 1! 2" 3№ 4% 5: 6, 7. 8; 9( 0) -_ =+ \/ ёЁ

;; Й Ц У К Е Н Г Ш Щ З Х Ъ

;; Ф Ы В А П Р О Л Д Ж Э

;; Я Ч С М И Т Ь Б Ю /?

(quail-define-rules

("1" ?1)

("2" ?2)

("3" ?3)

("4" ?4)

("5" ?5)

("6" ?6)

("7" ?7)

("8" ?8)

("9" ?9)

("0" ?0)

("-" ?-)

("=" ?=)

("|" ?Ё)

("`" ?])

("q" ?й)

("w" ?ц)

("e" ?у)

("r" ?к)

("t" ?е)

("y" ?н)

("u" ?г)

("i" ?ш)

("o" ?щ)

("p" ?з)

("[" ?х)

("]" ?ъ)

("a" ?ф)

("s" ?ы)

("d" ?в)

("f" ?а)

("g" ?п)

("h" ?р)

("j" ?о)

("k" ?л)

("l" ?д)

(";" ?ж)

("'" ?э)

("\\" ?\ё)

("z" ?я)

("x" ?ч)

("c" ?с)

("v" ?м)

("b" ?и)

("n" ?т)

("m" ?ь)

("," ?б)

("." ?ю)

("/" ?/)

("!" ?!)

("@" ?\")

("#" ?№)

("$" ?\%)

("%" ?:)

("^" ?,)

("&" ?.)

("*" ?\;)

("(" ?()

(")" ?))

("_" ?_)

("+" ?+)

("~" ?[)

("Q" ?Й)

("W" ?Ц)

("E" ?У)

("R" ?К)

("T" ?Е)

("Y" ?Н)

("U" ?Г)

("I" ?Ш)

("O" ?Щ)

("P" ?З)

("{" ?Х)

("}" ?Ъ)

("A" ?Ф)

("S" ?Ы)

("D" ?В)

("F" ?А)

("G" ?П)

("H" ?Р)

("J" ?О)

("K" ?Л)

("L" ?Д)

(":" ?Ж)

("\"" ?Э)

("|" ?Ё)

("Z" ?Я)

("X" ?Ч)

("C" ?С)

("V" ?М)

("B" ?И)

("N" ?Т)

("M" ?Ь)

("<" ?Б)

(">" ?Ю)

("?" ??)

("§" ?<)

("±" ?>)

)

(global-set-key (kbd "M-2") '(lambda() (interactive) (insert "@")))

(global-set-key (kbd "M-3") '(lambda() (interactive) (insert "#")))

(global-set-key (kbd "M-4") '(lambda() (interactive) (insert "$")))

(global-set-key (kbd "M-5") '(lambda() (interactive) (insert "%")))

(global-set-key (kbd "M-6") '(lambda() (interactive) (insert "^")))

(global-set-key (kbd "M-7") '(lambda() (interactive) (insert "&")))

(global-set-key (kbd "M-8") '(lambda() (interactive) (insert "*")))

(global-set-key (kbd "M--") '(lambda() (interactive) (insert "—")))

;; Local Variables:

;; coding: utf-8

;; End:

;;; russian-nowinkeys.el ends here

(provide 'russian-no-windows)

;;========================================================

Here is my flyspell rules:

(add-to-list

'ispell-local-dictionary-alist

'("russian" ; combo english+russian

"[a-zA-ZАБВГДЕЁЖЗИЙКЛМНОПРСТУФХЦЧШЩЬЫЪЭЮЯабвгдеёжзийклмнопрстуфхцчшщьыъэюя]"

"[^a-zA-ZАБВГДЕЁЖЗИЙКЛМНОПРСТУФХЦЧШЩЬЫЪЭЮЯабвгдеёжзийклмнопрстуфхцчшщьыъэюя]"

"[-']"

nil

("-d" "en_US,ru_RU")

nil utf-8))

When flyspell mode is turned off everything works OK, but with flyspell turned on I get strange behavior of "," and "." symbols which are mapped to "^" and "&" (which are Shift+6 and shift+7. Usually I want type "," at the end of the word and it doesn't work. "б" typed instead. But when I type shift+6 in the beginning of the word, I am getting ",", but any subsequent shift+6 gives me "б" again.

What I want:

Здравствуйте, товарищ!

What I got:

Здравствуйтеб товарищ!

I believe it related to fact that I have rules "^" -> "," and "," -> "б", but on emacs 24.3 everything worked just fine and still working without flyspell.

Thanks in advance,

Sergei